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/7916143/working' mkdir: created directory `/scratch/stefan/7916143/working/protonate' Storing results in /scratch/stefan/7916143/finished Working in /scratch/stefan/7916143/working /scratch/stefan/7916143/working /scratch/stefan/7916143 /scratch/stefan/7916143/working/protonate /scratch/stefan/7916143/working /scratch/stefan/7916143 Precomputing protomers for all compounds (pH: 7.4) awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot move `/nfs/home/stefan/.install4j_new' to `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory ph 7.4: 1056 protomers created Coalesing and merging protomers 1025 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1029 protomers after new stereo-center expansion /scratch/stefan/7916143/working /scratch/stefan/7916143 Bulk generating 3D conformations all protomers in /scratch/stefan/7916143/working/3D mkdir: created directory `/scratch/stefan/7916143/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7916143/working/protonate/xaaaaax-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' 1030 3D conformations generated for 1000 compounds Building REAL250005060893 mkdir: created directory `/scratch/stefan/7916143/working/building' mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060893' /scratch/stefan/7916143/working/building/REAL250005060893 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060893 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060893/0 /scratch/stefan/7916143/working/building/REAL250005060893 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1 `/scratch/stefan/7916143/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1)C1=CCC1) `REAL250005060893.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060893 none O=C(NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1)C1=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 10, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 26, 36, 36, 36, 26, 10, 10, 1, 1, 1, 1, 1, 1, 20, 36, 36, 36, 36, 36] 54 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060893 none O=C(NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1)C1=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 41, 20, 20, 20, 20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 41, 41, 20, 20, 20, 20, 20, 20, 1, 54, 54, 54, 54, 54] 54 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 170 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060893 none O=C(NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1)C1=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 21, 36, 36, 36, 36, 36, 36, 47, 47, 54, 54, 54, 54, 54, 1, 1, 1, 1, 7, 21, 21, 36, 36, 36, 36, 36, 36, 54, 1, 1, 1, 1, 1] 54 rigid atoms, others: [32, 1, 34, 35, 36, 33, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 168 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060893 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060893 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `/scratch/stefan/7916143/finished' Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060893/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060893 Building REAL250005060894 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060894' /scratch/stefan/7916143/working/building/REAL250005060894 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060894 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060894/0 /scratch/stefan/7916143/working/building/REAL250005060894 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/2 `/scratch/stefan/7916143/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060894.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060894 none CC(CF)C(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 26, 107, 159, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 107, 107, 107, 107, 159, 159, 26, 9, 9, 1, 1, 1, 1, 1, 1, 20] 201 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 673 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060894 none CC(CF)C(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 104, 197, 201, 104, 104, 54, 20, 20, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 201, 201, 104, 54, 54, 20, 20, 20, 20, 20, 20, 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: 785 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060894 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060894 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060894/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060894 Building REAL250005060895 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060895' /scratch/stefan/7916143/working/building/REAL250005060895 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060895 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060895/0 /scratch/stefan/7916143/working/building/REAL250005060895 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/3 `/scratch/stefan/7916143/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060895.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060895 none CC=CC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [58, 58, 25, 25, 25, 10, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 58, 58, 58, 58, 58, 25, 10, 10, 1, 1, 1, 1, 1, 1, 22] 94 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060895 none CC=CC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 78, 78, 78, 59, 22, 22, 22, 22, 22, 22, 11, 1, 11, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 78, 59, 59, 22, 22, 22, 22, 22, 22, 1] 94 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: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060895 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060895 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060895/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060895 Building REAL250005060896 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060896' /scratch/stefan/7916143/working/building/REAL250005060896 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060896 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060896/0 /scratch/stefan/7916143/working/building/REAL250005060896 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/4 `/scratch/stefan/7916143/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CCF)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060896.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060896 none O=C(C=CCF)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 7, 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] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 19, 53, 53, 84, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 53, 53, 84, 84, 19, 7, 7, 1, 1, 1, 1, 1, 1, 20] 104 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060896 none O=C(C=CCF)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 7, 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] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [74, 74, 74, 97, 97, 104, 42, 20, 20, 20, 20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 97, 97, 104, 104, 74, 42, 42, 20, 20, 20, 20, 20, 20, 1] 104 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: 367 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060896 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060896 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060896/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060896 Building REAL250005060897 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060897' /scratch/stefan/7916143/working/building/REAL250005060897 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005060897 as failed and skipping /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `/scratch/stefan/7916143/failed' `/scratch/stefan/7916143/working/building/REAL250005060897' -> `/scratch/stefan/7916143/failed/REAL250005060897' Building REAL250005060898 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060898' /scratch/stefan/7916143/working/building/REAL250005060898 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060898 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060898/0 /scratch/stefan/7916143/working/building/REAL250005060898 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/5 `/scratch/stefan/7916143/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060898.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060898 none C[C@H](O)C(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 396 conformations in input total number of sets (complete confs): 396 using faster count positions algorithm for large data unique positions, atoms: [94, 34, 94, 94, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 94, 94, 94, 282, 34, 9, 9, 1, 1, 1, 1, 1, 1, 23] 396 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 648 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060898 none C[C@H](O)C(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 396 conformations in input total number of sets (complete confs): 396 using faster count positions algorithm for large data unique positions, atoms: [132, 116, 132, 132, 116, 116, 66, 23, 23, 23, 23, 23, 23, 11, 1, 11, 1, 1, 1, 1, 1, 1, 132, 132, 132, 396, 116, 66, 66, 23, 23, 23, 23, 23, 23, 1] 396 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: 877 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060898 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060898 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060898/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060898 Building REAL250005060899 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060899' /scratch/stefan/7916143/working/building/REAL250005060899 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060899 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060899/0 /scratch/stefan/7916143/working/building/REAL250005060899 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/6 `/scratch/stefan/7916143/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060899.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060899 none CON=CC(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [110, 97, 97, 36, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 110, 110, 110, 97, 36, 9, 9, 1, 1, 1, 1, 1, 1, 24] 144 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060899 none CON=CC(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 124, 124, 124, 67, 24, 24, 24, 24, 24, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 124, 67, 67, 24, 24, 24, 24, 24, 24, 1] 144 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: 483 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060899 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060899 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060899/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060899 Building REAL250005060900 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060900' /scratch/stefan/7916143/working/building/REAL250005060900 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060900 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060900/0 /scratch/stefan/7916143/working/building/REAL250005060900 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/7 `/scratch/stefan/7916143/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060900.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060900 none C[C@@H]1C[C@H]1C(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 12, 63, 116, 116, 116, 116, 116, 116, 160, 160, 181, 181, 181, 181, 181, 2, 2, 2, 1, 1, 12, 63, 63, 116, 116, 116, 116, 116, 116, 181] 181 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 27, 28] set([7, 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, 38]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060900 none C[C@@H]1C[C@H]1C(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [116, 116, 116, 116, 30, 116, 30, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 116, 116, 116, 116, 116, 30, 9, 9, 1, 1, 1, 1, 1, 1, 23] 181 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38]) total number of confs: 333 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005060900 none C[C@@H]1C[C@H]1C(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 103, 181, 103, 103, 69, 23, 23, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 181, 181, 181, 181, 181, 103, 69, 69, 23, 23, 23, 23, 23, 23, 1] 181 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: 614 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060900 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060900 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060900/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060900 Building REAL250005060901 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060901' /scratch/stefan/7916143/working/building/REAL250005060901 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060901 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060901/0 /scratch/stefan/7916143/working/building/REAL250005060901 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/8 `/scratch/stefan/7916143/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)C(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060901.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060901 none CC(C)(O)C(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 12, 1, 11, 8, 5, 5, 7, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 468 conformations in input total number of sets (complete confs): 468 using faster count positions algorithm for large data unique positions, atoms: [96, 34, 96, 95, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 96, 96, 96, 96, 96, 96, 288, 34, 9, 9, 1, 1, 1, 1, 1, 1, 24] 468 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38]) total number of confs: 667 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060901 none CC(C)(O)C(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 12, 1, 11, 8, 5, 5, 7, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 468 conformations in input total number of sets (complete confs): 468 using faster count positions algorithm for large data unique positions, atoms: [156, 129, 156, 156, 129, 129, 75, 24, 24, 24, 24, 24, 24, 11, 1, 11, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 156, 468, 129, 75, 75, 24, 24, 24, 24, 24, 24, 1] 468 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: 1041 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060901 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060901 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060901/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060901 Building REAL250005060902 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060902' /scratch/stefan/7916143/working/building/REAL250005060902 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060902 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060902/0 /scratch/stefan/7916143/working/building/REAL250005060902 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/9 `/scratch/stefan/7916143/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060902.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060902 none C=C(C)CC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 114, 150, 23, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 150, 150, 150, 150, 150, 114, 114, 23, 8, 8, 1, 1, 1, 1, 1, 1, 22] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38]) total number of confs: 545 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060902 none C=C(C)CC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 112, 112, 112, 62, 22, 22, 22, 22, 22, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 112, 62, 62, 22, 22, 22, 22, 22, 22, 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: 790 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060902 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060902 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060902/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060902 Building REAL250005060903 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060903' /scratch/stefan/7916143/working/building/REAL250005060903 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060903 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060903/0 /scratch/stefan/7916143/working/building/REAL250005060903 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/10 `/scratch/stefan/7916143/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060903.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060903 none C=CCC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 108, 23, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 145, 145, 145, 108, 108, 23, 9, 9, 1, 1, 1, 1, 1, 1, 24] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 546 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060903 none C=CCC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 24, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 121, 71, 71, 24, 24, 24, 24, 24, 24, 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: 816 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060903 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060903 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060903/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060903 Building REAL250005060904 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060904' /scratch/stefan/7916143/working/building/REAL250005060904 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005060904 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060904/0 /scratch/stefan/7916143/working/building/REAL250005060904 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/11 `/scratch/stefan/7916143/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060904.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060904 none C[NH+](C)CC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 17, 17, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 8, 3, 3, 1, 1, 1, 1, 1, 1, 13] 23 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060904 none C[NH+](C)CC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 21, 21, 21, 17, 13, 13, 13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 21, 17, 17, 13, 13, 13, 13, 13, 13, 1] 23 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: 77 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060904 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005060904/1 /scratch/stefan/7916143/working/building/REAL250005060904 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/12 `/scratch/stefan/7916143/working/3D/12' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060904.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005060904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060904 none CN(C)CC(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 123, 145, 36, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 145, 145, 145, 145, 145, 145, 123, 123, 36, 9, 9, 1, 1, 1, 1, 1, 1, 21] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39]) total number of confs: 538 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060904 none CN(C)CC(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 201, 124, 124, 124, 64, 21, 21, 21, 21, 21, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 197, 197, 124, 64, 64, 21, 21, 21, 21, 21, 21, 1] 201 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: 787 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060904 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060904 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060904/0.* 1: /scratch/stefan/7916143/working/building/REAL250005060904/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060904 Building REAL250005060905 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060905' /scratch/stefan/7916143/working/building/REAL250005060905 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060905 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060905/0 /scratch/stefan/7916143/working/building/REAL250005060905 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/13 `/scratch/stefan/7916143/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060905.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060905 none N#CCC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 24, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 77, 77, 24, 9, 9, 1, 1, 1, 1, 1, 1, 22] 111 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060905 none N#CCC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 75, 75, 75, 47, 22, 22, 22, 22, 22, 22, 11, 1, 11, 1, 1, 1, 1, 1, 1, 111, 111, 75, 47, 47, 22, 22, 22, 22, 22, 22, 1] 111 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: 427 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060905 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060905 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060905/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060905 Building REAL250005060906 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060906' /scratch/stefan/7916143/working/building/REAL250005060906 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060906 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060906/0 /scratch/stefan/7916143/working/building/REAL250005060906 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/14 `/scratch/stefan/7916143/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1)C1CC1F) `REAL250005060906.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060906 none O=C(NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1)C1CC1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 31, 107, 107, 107, 31, 9, 9, 1, 1, 1, 1, 1, 1, 24, 107, 107, 107, 107] 165 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060906 none O=C(NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1)C1CC1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 59, 24, 24, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 102, 165, 165, 165, 102, 59, 59, 24, 24, 24, 24, 24, 24, 1, 165, 165, 165, 165] 165 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: 535 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005060906 none O=C(NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1)C1CC1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 63, 107, 107, 107, 107, 107, 107, 148, 148, 165, 165, 165, 165, 165, 1, 1, 1, 1, 12, 63, 63, 107, 107, 107, 107, 107, 107, 165, 1, 1, 1, 1] 165 rigid atoms, others: [32, 1, 34, 35, 33, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 540 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060906 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060906 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060906/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060906 Building REAL250005060907 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060907' /scratch/stefan/7916143/working/building/REAL250005060907 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060907 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060907/0 /scratch/stefan/7916143/working/building/REAL250005060907 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/15 `/scratch/stefan/7916143/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060907.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060907 none O=C(CCF)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 7, 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] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 110, 145, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 110, 110, 145, 145, 25, 9, 9, 1, 1, 1, 1, 1, 1, 22] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 611 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060907 none O=C(CCF)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 7, 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] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 201, 201, 59, 22, 22, 22, 22, 22, 22, 11, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 110, 59, 59, 22, 22, 22, 22, 22, 22, 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: 793 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060907 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060907 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060907/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060907 Building REAL250005060908 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060908' /scratch/stefan/7916143/working/building/REAL250005060908 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060908 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060908/0 /scratch/stefan/7916143/working/building/REAL250005060908 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/16 `/scratch/stefan/7916143/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060908.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060908 none CO[C@H](C)C(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 124, 30, 124, 124, 30, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 139, 139, 139, 124, 124, 124, 30, 9, 9, 1, 1, 1, 1, 1, 1, 27] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38]) total number of confs: 499 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060908 none CO[C@H](C)C(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 136, 200, 200, 136, 136, 72, 27, 27, 27, 27, 27, 27, 11, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 200, 200, 136, 72, 72, 27, 27, 27, 27, 27, 27, 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: 755 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060908 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060908 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060908/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060908 Building REAL250005060909 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060909' /scratch/stefan/7916143/working/building/REAL250005060909 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060909 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060909/0 /scratch/stefan/7916143/working/building/REAL250005060909 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/17 `/scratch/stefan/7916143/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060909.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060909 none C[C@@H](O)C(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 387 conformations in input total number of sets (complete confs): 387 using faster count positions algorithm for large data unique positions, atoms: [90, 35, 90, 90, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 90, 90, 90, 270, 35, 9, 9, 1, 1, 1, 1, 1, 1, 26] 387 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 629 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060909 none C[C@@H](O)C(=O)NC[C@H]1CCCN1C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 387 conformations in input total number of sets (complete confs): 387 using faster count positions algorithm for large data unique positions, atoms: [129, 113, 129, 129, 113, 113, 74, 26, 26, 26, 26, 26, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 129, 129, 129, 387, 113, 74, 74, 26, 26, 26, 26, 26, 26, 1] 387 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: 861 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060909 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060909 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060909/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060909 Building REAL250005060910 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060910' /scratch/stefan/7916143/working/building/REAL250005060910 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060910 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060910/0 /scratch/stefan/7916143/working/building/REAL250005060910 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/18 `/scratch/stefan/7916143/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060910.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060910 none C=C1CC1C(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 65, 110, 110, 110, 110, 110, 110, 151, 151, 164, 164, 164, 164, 164, 1, 1, 1, 1, 1, 13, 65, 65, 110, 110, 110, 110, 110, 110, 164] 164 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 550 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060910 none C=C1CC1C(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [110, 110, 110, 27, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 110, 110, 110, 110, 110, 27, 9, 9, 1, 1, 1, 1, 1, 1, 22] 164 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 316 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060910 none C=C1CC1C(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 89, 89, 89, 54, 22, 22, 22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 89, 54, 54, 22, 22, 22, 22, 22, 22, 1] 164 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: 529 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060910 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060910 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060910/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060910 Building REAL250005060911 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060911' /scratch/stefan/7916143/working/building/REAL250005060911 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060911 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060911/0 /scratch/stefan/7916143/working/building/REAL250005060911 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/19 `/scratch/stefan/7916143/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060911.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060911 none CC1=CC1C(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 5, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 71, 129, 129, 129, 129, 129, 129, 182, 182, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 13, 71, 71, 129, 129, 129, 129, 129, 129, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 659 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060911 none CC1=CC1C(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 5, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 28, 28, 28, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 129, 129, 129, 129, 129, 28, 9, 9, 1, 1, 1, 1, 1, 1, 23] 201 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 361 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005060911 none CC1=CC1C(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 5, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 113, 113, 113, 63, 23, 23, 23, 23, 23, 23, 11, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 113, 63, 63, 23, 23, 23, 23, 23, 23, 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: 652 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060911 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060911 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060911/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060911 Building REAL250005060912 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060912' /scratch/stefan/7916143/working/building/REAL250005060912 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060912 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060912/0 /scratch/stefan/7916143/working/building/REAL250005060912 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/20 `/scratch/stefan/7916143/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005060912.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060912 none C=CC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 26, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 49, 49, 49, 26, 9, 9, 1, 1, 1, 1, 1, 1, 22] 77 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060912 none C=CC(=O)NC[C@H]1CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 57, 22, 22, 22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 57, 57, 22, 22, 22, 22, 22, 22, 1] 77 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: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060912 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060912 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060912/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060912 Building REAL250005060913 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060913' /scratch/stefan/7916143/working/building/REAL250005060913 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060913 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060913/0 /scratch/stefan/7916143/working/building/REAL250005060913 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/21 `/scratch/stefan/7916143/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060913.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060913 none CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 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, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 151, 151, 151, 111, 52, 22, 50, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 151, 111, 110, 54, 54, 54, 54, 22, 22, 5, 1] 201 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 917 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060913 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060913 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060913/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060913 Building REAL250005060914 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060914' /scratch/stefan/7916143/working/building/REAL250005060914 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060914 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060914/0 /scratch/stefan/7916143/working/building/REAL250005060914 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/22 `/scratch/stefan/7916143/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060914.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060914 none COCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 191, 90, 90, 90, 50, 24, 9, 23, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 191, 90, 50, 50, 25, 25, 25, 25, 9, 9, 3, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 870 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060914 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060914 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060914/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060914 Building REAL250005060915 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060915' /scratch/stefan/7916143/working/building/REAL250005060915 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060915 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060915/0 /scratch/stefan/7916143/working/building/REAL250005060915 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/23 `/scratch/stefan/7916143/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1) `REAL250005060915.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060915 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 38, 78, 102, 102, 102, 201, 201, 38, 38, 38, 38, 15, 15, 4, 1, 78, 78, 102, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 26] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060915 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 41, 86, 148, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 11, 1, 1, 1, 88, 88, 88, 88, 148, 148, 201, 201, 41, 41, 11, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 852 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060915 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060915 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060915/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060915 Building REAL250005060916 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060916' /scratch/stefan/7916143/working/building/REAL250005060916 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060916 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060916/0 /scratch/stefan/7916143/working/building/REAL250005060916 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/24 `/scratch/stefan/7916143/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCC1) `REAL250005060916.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060916 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 38, 75, 101, 101, 101, 201, 201, 201, 38, 38, 38, 38, 16, 16, 4, 1, 75, 75, 101, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 715 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060916 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 81, 152, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 1, 10, 1, 1, 1, 1, 81, 81, 81, 81, 152, 152, 201, 201, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 869 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060916 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060916 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060916/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060916 Building REAL250005060917 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060917' /scratch/stefan/7916143/working/building/REAL250005060917 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060917 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060917/0 /scratch/stefan/7916143/working/building/REAL250005060917 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/25 `/scratch/stefan/7916143/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCCC1) `REAL250005060917.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060917 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 33, 76, 113, 113, 113, 201, 201, 201, 201, 33, 33, 33, 33, 13, 13, 3, 1, 76, 76, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 731 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060917 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 84, 155, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 9, 1, 1, 1, 1, 1, 85, 85, 85, 85, 155, 155, 201, 201, 42, 42, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 885 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060917 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060917 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060917/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060917 Building REAL250005060918 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060918' /scratch/stefan/7916143/working/building/REAL250005060918 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060918 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060918/0 /scratch/stefan/7916143/working/building/REAL250005060918 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/26 `/scratch/stefan/7916143/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1CC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060918.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060918 none CC(CNC(=O)CC1CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 84, 23, 23, 3, 23, 1, 1, 1, 1, 125, 169, 201, 201, 201, 201, 201, 201, 201, 201, 125, 125, 125, 125, 84, 84, 23, 3, 3, 1, 1, 1, 1, 1, 169, 169, 201, 201] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060918 none CC(CNC(=O)CC1CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 27, 60, 83, 83, 83, 162, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 60, 60, 83, 162, 162, 201, 201, 201, 201, 201, 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: 893 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060918 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060918 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060918/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060918 Building REAL250005060919 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060919' /scratch/stefan/7916143/working/building/REAL250005060919 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060919 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060919/0 /scratch/stefan/7916143/working/building/REAL250005060919 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/27 `/scratch/stefan/7916143/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)F) `REAL250005060919.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060919 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 14, 21, 21, 21, 44, 44, 44, 11, 11, 11, 11, 9, 9, 4, 1, 14, 14, 21, 44, 44, 44, 44, 44, 44] 44 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060919 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060919 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060919/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060919 Building REAL250005060920 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060920' /scratch/stefan/7916143/working/building/REAL250005060920 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060920 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060920/0 /scratch/stefan/7916143/working/building/REAL250005060920 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/28 `/scratch/stefan/7916143/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(F)F) `REAL250005060920.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060920 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 20, 20, 20, 7, 7, 7, 7, 5, 5, 4, 1, 7, 7, 9, 20, 20, 20] 20 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060920 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060920 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060920/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060920 Building REAL250005060921 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060921' /scratch/stefan/7916143/working/building/REAL250005060921 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060921 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060921/0 /scratch/stefan/7916143/working/building/REAL250005060921 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/29 `/scratch/stefan/7916143/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060921.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060921 none COCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 135, 135, 135, 67, 32, 11, 32, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 135, 67, 67, 34, 34, 34, 34, 11, 11, 3, 1] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 844 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060921 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060921 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060921/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060921 Building REAL250005060922 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060922' /scratch/stefan/7916143/working/building/REAL250005060922 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060922 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060922/0 /scratch/stefan/7916143/working/building/REAL250005060922 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/30 `/scratch/stefan/7916143/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060922.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060922 none CCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 102, 102, 102, 61, 31, 12, 28, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 191, 102, 61, 61, 31, 31, 31, 31, 12, 12, 4, 1] 201 rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 872 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060922 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060922 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060922/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060922 Building REAL250005060923 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060923' /scratch/stefan/7916143/working/building/REAL250005060923 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060923 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060923/0 /scratch/stefan/7916143/working/building/REAL250005060923 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/31 `/scratch/stefan/7916143/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=CO1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060923.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060923 none CC(CNC(=O)C1=CC=CO1)CNC(=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', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 6, 6, 1, 6, 1, 1, 1, 1, 1, 77, 150, 200, 200, 200, 201, 201, 201, 201, 201, 79, 79, 79, 79, 30, 30, 7, 1, 1, 1, 150, 150, 200, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 849 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060923 none CC(CNC(=O)C1=CC=CO1)CNC(=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', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 64, 130, 180, 180, 180, 201, 201, 201, 201, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 128, 129, 180, 201, 201, 201, 28, 28, 7, 1] 201 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 773 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060923 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060923 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060923/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060923 Building REAL250005060924 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060924' /scratch/stefan/7916143/working/building/REAL250005060924 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060924 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060924/0 /scratch/stefan/7916143/working/building/REAL250005060924 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/32 `/scratch/stefan/7916143/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060924.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060924 none CC(=O)NCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 201, 198, 107, 107, 107, 59, 27, 10, 24, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 198, 198, 107, 59, 59, 27, 27, 27, 27, 10, 10, 3, 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: 840 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060924 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060924 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060924/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060924 Building REAL250005060925 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060925' /scratch/stefan/7916143/working/building/REAL250005060925 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060925 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060925/0 /scratch/stefan/7916143/working/building/REAL250005060925 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/33 `/scratch/stefan/7916143/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060925.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060925 none CC(C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 201, 201, 128, 128, 128, 74, 37, 14, 34, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 74, 74, 37, 37, 37, 37, 14, 14, 4, 1] 201 rigid atoms, others: [39, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 866 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060925 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060925 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060925/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060925 Building REAL250005060926 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060926' /scratch/stefan/7916143/working/building/REAL250005060926 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060926 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060926/0 /scratch/stefan/7916143/working/building/REAL250005060926 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/34 `/scratch/stefan/7916143/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1C) `REAL250005060926.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060926 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 33, 68, 102, 102, 102, 201, 201, 201, 33, 33, 33, 33, 13, 13, 4, 1, 68, 68, 102, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060926 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 52, 90, 152, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 1, 13, 1, 1, 1, 1, 91, 91, 91, 91, 152, 151, 201, 201, 52, 52, 13, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 852 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060926 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060926 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060926/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060926 Building REAL250005060927 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060927' /scratch/stefan/7916143/working/building/REAL250005060927 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060927 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060927/0 /scratch/stefan/7916143/working/building/REAL250005060927 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/35 `/scratch/stefan/7916143/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060927.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060927 none CCOCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 201, 197, 95, 95, 95, 50, 26, 11, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 197, 95, 50, 50, 26, 26, 26, 26, 11, 11, 4, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 862 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060927 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060927 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060927/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060927 Building REAL250005060928 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060928' /scratch/stefan/7916143/working/building/REAL250005060928 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060928 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060928/0 /scratch/stefan/7916143/working/building/REAL250005060928 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/36 `/scratch/stefan/7916143/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060928.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060928 none CC(C)=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 158, 158, 158, 104, 50, 20, 48, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 158, 104, 104, 51, 51, 51, 51, 20, 20, 4, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 794 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060928 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060928 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060928/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060928 Building REAL250005060929 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060929' /scratch/stefan/7916143/working/building/REAL250005060929 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060929 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060929/0 /scratch/stefan/7916143/working/building/REAL250005060929 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/37 `/scratch/stefan/7916143/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCCO1) `REAL250005060929.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060929 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [21, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 21, 32, 46, 46, 46, 82, 82, 82, 82, 21, 21, 21, 21, 15, 15, 5, 1, 32, 32, 46, 82, 82, 82, 82, 82, 82, 82] 82 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 292 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060929 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [60, 44, 59, 77, 82, 82, 82, 82, 82, 82, 82, 82, 12, 12, 1, 12, 1, 1, 1, 1, 1, 60, 60, 60, 60, 77, 77, 82, 82, 44, 44, 12, 1, 1, 1, 1, 1, 1, 1] 82 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 370 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060929 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060929 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060929/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060929 Building REAL250005060930 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060930' /scratch/stefan/7916143/working/building/REAL250005060930 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060930 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060930/0 /scratch/stefan/7916143/working/building/REAL250005060930 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/38 `/scratch/stefan/7916143/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060930.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060930 none CSCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 124, 124, 124, 65, 29, 11, 28, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 189, 189, 124, 65, 65, 30, 30, 30, 30, 11, 11, 3, 1] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 805 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060930 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060930 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060930/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060930 Building REAL250005060931 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060931' /scratch/stefan/7916143/working/building/REAL250005060931 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060931 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060931/0 /scratch/stefan/7916143/working/building/REAL250005060931 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/39 `/scratch/stefan/7916143/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060931.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060931 none CC(C)CCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 199, 201, 187, 79, 79, 79, 45, 22, 9, 22, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 200, 201, 201, 201, 201, 199, 199, 187, 187, 79, 45, 45, 22, 22, 22, 22, 9, 9, 3, 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: 882 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060931 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060931 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060931/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060931 Building REAL250005060932 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060932' /scratch/stefan/7916143/working/building/REAL250005060932 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060932 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060932/0 /scratch/stefan/7916143/working/building/REAL250005060932 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/40 `/scratch/stefan/7916143/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=CN1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060932.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060932 none CC(CNC(=O)C1=CC=CN1)CNC(=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', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 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: [77, 33, 7, 7, 1, 7, 1, 1, 1, 1, 1, 77, 149, 200, 200, 200, 201, 201, 201, 201, 201, 80, 80, 80, 80, 33, 33, 7, 1, 1, 1, 1, 149, 148, 200, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 838 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060932 none CC(CNC(=O)C1=CC=CN1)CNC(=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', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 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: [55, 26, 55, 118, 173, 173, 173, 201, 201, 201, 201, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 116, 118, 173, 201, 201, 201, 201, 26, 26, 6, 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: 746 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060932 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060932 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060932/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060932 Building REAL250005060933 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060933' /scratch/stefan/7916143/working/building/REAL250005060933 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060933 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060933/0 /scratch/stefan/7916143/working/building/REAL250005060933 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/41 `/scratch/stefan/7916143/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=COC=C1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060933.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060933 none CC(CNC(=O)C1=COC=C1)CNC(=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', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 5, 5, 1, 5, 1, 1, 1, 1, 1, 83, 157, 200, 200, 200, 201, 201, 201, 201, 201, 85, 85, 85, 85, 30, 30, 5, 1, 1, 1, 156, 157, 200, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060933 none CC(CNC(=O)C1=COC=C1)CNC(=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', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 41, 91, 140, 140, 140, 201, 201, 201, 201, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 91, 91, 140, 201, 201, 201, 19, 19, 5, 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: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060933 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060933 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060933/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060933 Building REAL250005060934 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060934' /scratch/stefan/7916143/working/building/REAL250005060934 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060934 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060934/0 /scratch/stefan/7916143/working/building/REAL250005060934 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/42 `/scratch/stefan/7916143/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060934.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060934 none CCCCCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 198, 189, 92, 92, 92, 68, 37, 18, 37, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 198, 198, 189, 189, 92, 68, 67, 39, 39, 39, 39, 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: 895 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060934 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060934 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060934/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060934 Building REAL250005060935 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060935' /scratch/stefan/7916143/working/building/REAL250005060935 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060935 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060935/0 /scratch/stefan/7916143/working/building/REAL250005060935 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/43 `/scratch/stefan/7916143/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC(C)(C)C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060935.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060935 none CC(CNC(=O)CC(C)(C)C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 46, 103, 157, 157, 157, 199, 201, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 102, 103, 157, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 19, 19, 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: 873 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060935 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060935 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060935/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060935 Building REAL250005060936 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060936' /scratch/stefan/7916143/working/building/REAL250005060936 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060936 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060936/0 /scratch/stefan/7916143/working/building/REAL250005060936 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/44 `/scratch/stefan/7916143/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060936.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060936 none CCCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 199, 187, 78, 78, 78, 45, 22, 10, 22, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 200, 201, 201, 201, 201, 199, 199, 187, 187, 78, 45, 45, 22, 22, 22, 22, 10, 10, 3, 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: 862 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060936 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060936 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060936/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060936 Building REAL250005060937 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060937' /scratch/stefan/7916143/working/building/REAL250005060937 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060937 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060937/0 /scratch/stefan/7916143/working/building/REAL250005060937 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/45 `/scratch/stefan/7916143/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060937.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060937 none CC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 134, 201, 134, 134, 95, 42, 18, 40, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 134, 94, 95, 43, 43, 43, 43, 18, 18, 4, 1] 201 rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 898 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060937 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060937 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060937/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060937 Building REAL250005060938 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060938' /scratch/stefan/7916143/working/building/REAL250005060938 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060938 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060938/0 /scratch/stefan/7916143/working/building/REAL250005060938 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/46 `/scratch/stefan/7916143/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060938.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060938 none CCC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 114, 192, 114, 114, 62, 31, 13, 29, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 192, 192, 192, 192, 114, 62, 62, 32, 32, 32, 32, 13, 13, 3, 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: 868 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060938 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060938 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060938/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060938 Building REAL250005060939 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060939' /scratch/stefan/7916143/working/building/REAL250005060939 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060939 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060939/0 /scratch/stefan/7916143/working/building/REAL250005060939 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/47 `/scratch/stefan/7916143/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060939.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060939 none CCC(CC)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 170, 133, 170, 196, 133, 133, 67, 32, 13, 30, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 170, 196, 196, 196, 196, 196, 133, 67, 67, 32, 32, 32, 32, 13, 13, 4, 1] 201 rigid atoms, others: [42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1008 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060939 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060939 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060939/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060939 Building REAL250005060940 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060940' /scratch/stefan/7916143/working/building/REAL250005060940 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060940 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060940/0 /scratch/stefan/7916143/working/building/REAL250005060940 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/48 `/scratch/stefan/7916143/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=NN1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060940.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060940 none CC(CNC(=O)C1=CC=NN1)CNC(=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', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [72, 33, 8, 8, 1, 8, 1, 1, 1, 1, 1, 71, 135, 185, 185, 185, 188, 188, 188, 188, 188, 75, 75, 75, 75, 33, 33, 8, 1, 1, 1, 135, 135, 185, 188] 188 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 784 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060940 none CC(CNC(=O)C1=CC=NN1)CNC(=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', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [60, 30, 61, 127, 166, 166, 166, 188, 188, 188, 188, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 125, 126, 166, 188, 188, 188, 30, 30, 9, 1] 188 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: 727 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060940 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060940 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060940/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060940 Building REAL250005060941 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060941' /scratch/stefan/7916143/working/building/REAL250005060941 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060941 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060941/0 /scratch/stefan/7916143/working/building/REAL250005060941 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/49 `/scratch/stefan/7916143/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060941.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060941 none CCOC(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 112, 199, 112, 112, 62, 28, 11, 27, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 199, 199, 199, 199, 112, 62, 62, 29, 29, 29, 29, 11, 11, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 844 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060941 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060941 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060941/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060941 Building REAL250005060942 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060942' /scratch/stefan/7916143/working/building/REAL250005060942 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060942 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060942/0 /scratch/stefan/7916143/working/building/REAL250005060942 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/50 `/scratch/stefan/7916143/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CNN=C1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060942.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060942 none CC(CNC(=O)C1=CNN=C1)CNC(=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', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [40, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 39, 74, 108, 108, 108, 109, 109, 109, 109, 109, 41, 41, 41, 41, 17, 17, 4, 1, 1, 1, 74, 74, 108, 109] 109 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060942 none CC(CNC(=O)C1=CNN=C1)CNC(=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', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 19, 43, 89, 115, 115, 115, 115, 115, 115, 115, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 89, 88, 115, 115, 115, 115, 19, 19, 6, 1] 115 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: 463 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060942 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060942 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060942/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060942 Building REAL250005060943 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060943' /scratch/stefan/7916143/working/building/REAL250005060943 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060943 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060943/0 /scratch/stefan/7916143/working/building/REAL250005060943 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/51 `/scratch/stefan/7916143/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060943.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060943 none COCCCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 159, 160, 66, 66, 66, 40, 30, 19, 30, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 194, 176, 176, 160, 160, 66, 40, 40, 30, 30, 30, 30, 19, 19, 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: 980 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060943 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060943 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060943/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060943 Building REAL250005060944 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060944' /scratch/stefan/7916143/working/building/REAL250005060944 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060944 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060944/0 /scratch/stefan/7916143/working/building/REAL250005060944 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/52 `/scratch/stefan/7916143/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NOC=C1) `REAL250005060944.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060944 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NOC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [24, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 24, 43, 57, 57, 57, 73, 73, 73, 73, 24, 24, 24, 24, 13, 13, 6, 1, 43, 43, 57, 73, 73] 73 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060944 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NOC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [40, 20, 40, 60, 72, 72, 72, 73, 73, 73, 73, 73, 7, 7, 1, 7, 1, 1, 1, 1, 1, 40, 40, 40, 40, 60, 60, 72, 73, 20, 20, 7, 1, 1] 73 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060944 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060944 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060944/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060944 Building REAL250005060945 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060945' /scratch/stefan/7916143/working/building/REAL250005060945 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060945 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060945/0 /scratch/stefan/7916143/working/building/REAL250005060945 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/53 `/scratch/stefan/7916143/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060945.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060945 none CCC=C(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 198, 97, 198, 97, 97, 61, 25, 11, 23, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 198, 198, 198, 198, 97, 61, 61, 26, 26, 26, 26, 11, 11, 3, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 708 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060945 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060945 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060945/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060945 Building REAL250005060946 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060946' /scratch/stefan/7916143/working/building/REAL250005060946 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060946 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060946/0 /scratch/stefan/7916143/working/building/REAL250005060946 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/54 `/scratch/stefan/7916143/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060946.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060946 none COC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 132, 199, 132, 132, 74, 37, 15, 37, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 199, 199, 199, 199, 132, 74, 74, 39, 39, 39, 39, 15, 15, 4, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 831 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060946 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060946 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060946/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060946 Building REAL250005060947 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060947' /scratch/stefan/7916143/working/building/REAL250005060947 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060947 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060947/0 /scratch/stefan/7916143/working/building/REAL250005060947 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/55 `/scratch/stefan/7916143/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060947.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060947 none CC(C)OCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 201, 154, 86, 86, 86, 44, 20, 8, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 154, 154, 86, 44, 44, 20, 20, 20, 20, 8, 8, 2, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 838 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060947 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060947 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060947/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060947 Building REAL250005060948 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060948' /scratch/stefan/7916143/working/building/REAL250005060948 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060948 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060948/0 /scratch/stefan/7916143/working/building/REAL250005060948 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/56 `/scratch/stefan/7916143/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060948.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060948 none CCCOCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 165, 147, 132, 83, 83, 83, 42, 22, 8, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 165, 165, 132, 132, 83, 42, 42, 22, 22, 22, 22, 8, 8, 2, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 944 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060948 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060948 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060948/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060948 Building REAL250005060949 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060949' /scratch/stefan/7916143/working/building/REAL250005060949 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060949 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060949/0 /scratch/stefan/7916143/working/building/REAL250005060949 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/57 `/scratch/stefan/7916143/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCOC1) `REAL250005060949.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060949 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 37, 78, 119, 119, 119, 201, 201, 201, 201, 37, 37, 37, 37, 14, 14, 4, 1, 78, 78, 119, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060949 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 39, 89, 151, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 9, 1, 1, 1, 1, 1, 92, 92, 92, 92, 150, 151, 201, 201, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 884 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060949 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060949 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060949/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060949 Building REAL250005060950 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060950' /scratch/stefan/7916143/working/building/REAL250005060950 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060950 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060950/0 /scratch/stefan/7916143/working/building/REAL250005060950 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/58 `/scratch/stefan/7916143/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060950.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060950 none CCC(OC)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 189, 123, 189, 190, 123, 123, 59, 29, 12, 29, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 189, 190, 190, 190, 123, 59, 59, 31, 31, 31, 31, 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: 892 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060950 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060950 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060950/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060950 Building REAL250005060951 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060951' /scratch/stefan/7916143/working/building/REAL250005060951 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060951 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060951/0 /scratch/stefan/7916143/working/building/REAL250005060951 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/59 `/scratch/stefan/7916143/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060951.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060951 none COC(C)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 193, 201, 88, 88, 88, 51, 23, 10, 22, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 193, 193, 88, 51, 51, 24, 24, 24, 24, 10, 10, 3, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 867 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060951 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060951 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060951/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060951 Building REAL250005060952 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060952' /scratch/stefan/7916143/working/building/REAL250005060952 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060952 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060952/0 /scratch/stefan/7916143/working/building/REAL250005060952 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/60 `/scratch/stefan/7916143/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060952.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060952 none C=CCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 188, 86, 86, 86, 50, 26, 10, 25, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 188, 188, 86, 50, 50, 26, 26, 26, 26, 10, 10, 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: 869 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060952 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060952 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060952/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060952 Building REAL250005060953 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060953' /scratch/stefan/7916143/working/building/REAL250005060953 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060953 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060953/0 /scratch/stefan/7916143/working/building/REAL250005060953 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/61 `/scratch/stefan/7916143/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060953.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060953 none CCOCCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 197, 116, 116, 116, 99, 54, 23, 55, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 198, 198, 197, 197, 116, 98, 99, 57, 57, 57, 57, 23, 23, 5, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 897 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060953 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060953 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060953/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060953 Building REAL250005060954 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060954' /scratch/stefan/7916143/working/building/REAL250005060954 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060954 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060954/0 /scratch/stefan/7916143/working/building/REAL250005060954 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/62 `/scratch/stefan/7916143/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060954.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060954 none COCC(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 186, 97, 186, 97, 97, 52, 25, 11, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 186, 186, 186, 186, 97, 52, 52, 26, 26, 26, 26, 11, 11, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 887 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060954 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060954 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060954/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060954 Building REAL250005060955 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060955' /scratch/stefan/7916143/working/building/REAL250005060955 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060955 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060955/0 /scratch/stefan/7916143/working/building/REAL250005060955 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/63 `/scratch/stefan/7916143/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060955.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060955 none C=CCOCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 100, 67, 67, 67, 32, 19, 8, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 100, 100, 67, 32, 32, 19, 19, 19, 19, 8, 8, 2, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 840 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060955 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060955 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060955/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060955 Building REAL250005060956 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060956' /scratch/stefan/7916143/working/building/REAL250005060956 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060956 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060956/0 /scratch/stefan/7916143/working/building/REAL250005060956 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/64 `/scratch/stefan/7916143/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=COC=N1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060956.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060956 none CC(CNC(=O)C1=COC=N1)CNC(=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', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 5, 5, 1, 5, 1, 1, 1, 1, 1, 62, 142, 194, 194, 194, 201, 201, 201, 201, 201, 67, 67, 67, 67, 24, 24, 5, 1, 1, 141, 142, 194, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 801 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060956 none CC(CNC(=O)C1=COC=N1)CNC(=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', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 79, 147, 200, 200, 200, 201, 201, 201, 201, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 145, 147, 200, 201, 201, 35, 35, 9, 1] 201 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 834 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060956 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060956 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060956/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060956 Building REAL250005060957 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060957' /scratch/stefan/7916143/working/building/REAL250005060957 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060957 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060957/0 /scratch/stefan/7916143/working/building/REAL250005060957 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/65 `/scratch/stefan/7916143/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060957.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060957 none CCCC(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 173, 88, 173, 88, 88, 49, 27, 12, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 173, 173, 173, 173, 88, 49, 49, 28, 28, 28, 28, 12, 12, 4, 1] 201 rigid atoms, others: [42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 922 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060957 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060957 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060957/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060957 Building REAL250005060958 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060958' /scratch/stefan/7916143/working/building/REAL250005060958 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060958 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060958/0 /scratch/stefan/7916143/working/building/REAL250005060958 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/66 `/scratch/stefan/7916143/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCC1CC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060958.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060958 none CC(CNC(=O)CCC1CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 111, 36, 36, 7, 36, 3, 1, 1, 1, 1, 145, 196, 201, 201, 201, 201, 201, 201, 201, 201, 145, 145, 145, 145, 111, 111, 36, 7, 7, 3, 3, 1, 1, 1, 1, 1, 196, 196, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40]) total number of confs: 920 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060958 none CC(CNC(=O)CCC1CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 18, 34, 58, 58, 58, 146, 157, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 34, 34, 58, 146, 146, 159, 159, 201, 201, 201, 201, 201, 11, 11, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 839 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060958 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060958 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060958/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060958 Building REAL250005060959 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060959' /scratch/stefan/7916143/working/building/REAL250005060959 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060959 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060959/0 /scratch/stefan/7916143/working/building/REAL250005060959 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/67 `/scratch/stefan/7916143/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC=CC1) `REAL250005060959.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060959 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 33, 72, 113, 113, 113, 201, 201, 201, 201, 34, 34, 34, 34, 13, 13, 4, 1, 72, 72, 113, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 720 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060959 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 94, 157, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 9, 1, 1, 1, 1, 1, 95, 95, 95, 95, 157, 157, 201, 201, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 889 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060959 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060959 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060959/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060959 Building REAL250005060960 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060960' /scratch/stefan/7916143/working/building/REAL250005060960 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060960 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060960/0 /scratch/stefan/7916143/working/building/REAL250005060960 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/68 `/scratch/stefan/7916143/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1CCC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060960.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060960 none CC(CNC(=O)CC1CCC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 92, 27, 27, 6, 27, 1, 1, 1, 1, 1, 129, 173, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 129, 129, 92, 92, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 173, 173, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40]) total number of confs: 876 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060960 none CC(CNC(=O)CC1CCC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 35, 63, 94, 94, 94, 158, 201, 201, 201, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 63, 63, 94, 158, 158, 201, 201, 201, 201, 201, 201, 201, 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: 888 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060960 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060960 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060960/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060960 Building REAL250005060961 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060961' /scratch/stefan/7916143/working/building/REAL250005060961 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060961 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060961/0 /scratch/stefan/7916143/working/building/REAL250005060961 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/69 `/scratch/stefan/7916143/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C1CC1) `REAL250005060961.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060961 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 33, 69, 113, 113, 113, 201, 201, 201, 201, 33, 33, 33, 33, 13, 13, 4, 1, 69, 69, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 850 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060961 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 106, 164, 201, 201, 201, 201, 201, 201, 201, 201, 15, 15, 3, 15, 1, 3, 1, 1, 1, 108, 108, 108, 108, 164, 163, 201, 201, 61, 61, 15, 3, 3, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 890 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060961 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060961 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060961/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060961 Building REAL250005060962 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060962' /scratch/stefan/7916143/working/building/REAL250005060962 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060962 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060962/0 /scratch/stefan/7916143/working/building/REAL250005060962 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/70 `/scratch/stefan/7916143/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060962.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060962 none CC=C(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 133, 201, 133, 133, 88, 38, 15, 36, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 133, 88, 88, 39, 39, 39, 39, 15, 15, 4, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060962 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060962 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060962/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060962 Building REAL250005060963 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060963' /scratch/stefan/7916143/working/building/REAL250005060963 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060963 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060963/0 /scratch/stefan/7916143/working/building/REAL250005060963 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/71 `/scratch/stefan/7916143/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(C)C1) `REAL250005060963.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060963 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 33, 73, 107, 107, 107, 201, 201, 201, 201, 33, 33, 33, 33, 13, 13, 4, 1, 73, 73, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 736 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060963 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 85, 150, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 9, 1, 1, 1, 1, 1, 86, 86, 86, 86, 150, 150, 201, 201, 40, 40, 9, 1, 1, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 39, 40, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 869 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060963 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060963 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060963/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060963 Building REAL250005060964 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060964' /scratch/stefan/7916143/working/building/REAL250005060964 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060964 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060964/0 /scratch/stefan/7916143/working/building/REAL250005060964 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/72 `/scratch/stefan/7916143/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=C1CCC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060964.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060964 none CC(CNC(=O)C=C1CCC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 43, 8, 8, 1, 8, 1, 1, 1, 1, 1, 93, 153, 201, 201, 201, 201, 201, 201, 201, 201, 96, 96, 96, 96, 43, 43, 8, 1, 1, 1, 1, 1, 1, 1, 153, 153, 201, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 900 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060964 none CC(CNC(=O)C=C1CCC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 13, 34, 82, 142, 142, 142, 201, 201, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 82, 82, 142, 201, 201, 201, 201, 201, 201, 201, 13, 13, 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: 742 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060964 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060964 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060964/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060964 Building REAL250005060965 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060965' /scratch/stefan/7916143/working/building/REAL250005060965 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060965 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060965/0 /scratch/stefan/7916143/working/building/REAL250005060965 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/73 `/scratch/stefan/7916143/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060965.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060965 none CC(C)=C(F)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 5, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 156, 201, 156, 156, 92, 44, 19, 43, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 156, 92, 92, 46, 46, 46, 46, 19, 19, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 775 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060965 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060965 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060965/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060965 Building REAL250005060966 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060966' /scratch/stefan/7916143/working/building/REAL250005060966 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060966 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060966/0 /scratch/stefan/7916143/working/building/REAL250005060966 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/74 `/scratch/stefan/7916143/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCCC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060966.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060966 none CC(CNC(=O)C1=CCCC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 38, 7, 7, 1, 7, 1, 1, 1, 1, 1, 90, 152, 198, 198, 198, 201, 201, 201, 201, 201, 92, 92, 92, 92, 38, 38, 7, 1, 1, 1, 1, 1, 1, 1, 152, 151, 198, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 857 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060966 none CC(CNC(=O)C1=CCCC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 33, 67, 142, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 141, 142, 201, 201, 201, 201, 201, 201, 201, 201, 33, 33, 9, 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: 816 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060966 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060966 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060966/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060966 Building REAL250005060967 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060967' /scratch/stefan/7916143/working/building/REAL250005060967 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060967 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060967/0 /scratch/stefan/7916143/working/building/REAL250005060967 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/75 `/scratch/stefan/7916143/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1(C)C) `REAL250005060967.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060967 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 43, 97, 155, 155, 155, 201, 201, 201, 201, 44, 44, 44, 44, 16, 16, 4, 1, 97, 97, 155, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 796 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060967 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 82, 149, 201, 201, 201, 201, 201, 201, 201, 201, 8, 8, 1, 8, 1, 1, 1, 1, 1, 87, 87, 87, 87, 149, 149, 201, 201, 36, 36, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 878 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060967 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060967 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060967/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060967 Building REAL250005060968 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060968' /scratch/stefan/7916143/working/building/REAL250005060968 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060968 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060968/0 /scratch/stefan/7916143/working/building/REAL250005060968 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/76 `/scratch/stefan/7916143/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CC1(C)C) `REAL250005060968.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060968 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 41, 97, 154, 154, 154, 201, 201, 201, 201, 201, 42, 42, 42, 42, 14, 14, 3, 1, 97, 97, 154, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 793 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060968 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 83, 146, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 146, 146, 201, 201, 36, 36, 9, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [33, 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, 35, 36, 37, 38, 39, 40]) total number of confs: 863 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060968 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060968 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060968/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060968 Building REAL250005060969 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060969' /scratch/stefan/7916143/working/building/REAL250005060969 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060969 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060969/0 /scratch/stefan/7916143/working/building/REAL250005060969 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/77 `/scratch/stefan/7916143/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1CCCO1) `REAL250005060969.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060969 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [22, 13, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 22, 33, 50, 50, 50, 85, 85, 85, 85, 85, 22, 22, 22, 22, 12, 12, 3, 1, 33, 33, 50, 85, 85, 85, 85, 85, 85] 85 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 313 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060969 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [62, 48, 61, 77, 85, 85, 85, 85, 85, 85, 85, 85, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 77, 76, 85, 85, 48, 48, 13, 1, 1, 1, 1, 1, 1] 85 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 365 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060969 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060969 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060969/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060969 Building REAL250005060970 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060970' /scratch/stefan/7916143/working/building/REAL250005060970 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060970 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060970/0 /scratch/stefan/7916143/working/building/REAL250005060970 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/78 `/scratch/stefan/7916143/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060970.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060970 none CCC(C)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 185, 199, 64, 64, 64, 38, 23, 9, 23, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 199, 199, 199, 199, 185, 185, 64, 38, 38, 23, 23, 23, 23, 9, 9, 3, 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: 834 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060970 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060970 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060970/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060970 Building REAL250005060971 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060971' /scratch/stefan/7916143/working/building/REAL250005060971 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060971 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060971/0 /scratch/stefan/7916143/working/building/REAL250005060971 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/79 `/scratch/stefan/7916143/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060971.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060971 none C#CCCCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 156, 56, 56, 56, 38, 24, 15, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 194, 196, 178, 178, 156, 156, 56, 38, 38, 26, 26, 26, 26, 15, 15, 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: 971 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060971 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060971 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060971/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060971 Building REAL250005060972 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060972' /scratch/stefan/7916143/working/building/REAL250005060972 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060972 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060972/0 /scratch/stefan/7916143/working/building/REAL250005060972 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/80 `/scratch/stefan/7916143/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC(C)(C)O)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060972.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060972 none CC(CNC(=O)CC(C)(C)O)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 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, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 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: [34, 15, 38, 81, 130, 130, 130, 189, 200, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 81, 81, 130, 189, 189, 201, 201, 201, 201, 201, 201, 603, 15, 15, 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: 1486 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060972 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060972 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060972/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060972 Building REAL250005060973 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060973' /scratch/stefan/7916143/working/building/REAL250005060973 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060973 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060973/0 /scratch/stefan/7916143/working/building/REAL250005060973 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/81 `/scratch/stefan/7916143/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060973.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060973 none CC(C)[C@@H](O)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 201, 128, 183, 183, 128, 128, 70, 34, 13, 31, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 549, 128, 70, 70, 35, 35, 35, 35, 13, 13, 4, 1] 603 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1444 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060973 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060973 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060973/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060973 Building REAL250005060974 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060974' /scratch/stefan/7916143/working/building/REAL250005060974 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060974 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060974/0 /scratch/stefan/7916143/working/building/REAL250005060974 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/82 `/scratch/stefan/7916143/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060974.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060974 none CCC(C)=CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 125, 125, 125, 93, 93, 93, 59, 26, 11, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 125, 125, 125, 125, 93, 59, 59, 26, 26, 26, 26, 11, 11, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 957 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060974 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060974 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060974/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060974 Building REAL250005060975 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060975' /scratch/stefan/7916143/working/building/REAL250005060975 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060975 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060975/0 /scratch/stefan/7916143/working/building/REAL250005060975 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/83 `/scratch/stefan/7916143/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C#CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060975.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060975 none CC(C)C#CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', '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, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 150, 60, 23, 61, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 149, 148, 64, 64, 64, 64, 23, 23, 6, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 807 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060975 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060975 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060975/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060975 Building REAL250005060976 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060976' /scratch/stefan/7916143/working/building/REAL250005060976 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060976 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060976/0 /scratch/stefan/7916143/working/building/REAL250005060976 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/84 `/scratch/stefan/7916143/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C#CC1CC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060976.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060976 none CC(CNC(=O)C#CC1CC1)CNC(=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.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 40, 131, 199, 199, 199, 201, 201, 201, 201, 201, 46, 46, 46, 46, 10, 10, 2, 1, 1, 1, 1, 1, 131, 130, 199, 201] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 790 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060976 none CC(CNC(=O)C#CC1CC1)CNC(=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.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 149, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 149, 149, 201, 201, 201, 201, 201, 201, 27, 27, 6, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 799 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060976 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060976 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060976/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060976 Building REAL250005060977 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060977' /scratch/stefan/7916143/working/building/REAL250005060977 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060977 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060977/0 /scratch/stefan/7916143/working/building/REAL250005060977 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/85 `/scratch/stefan/7916143/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060977.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060977 none C=C(C)CCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 190, 87, 87, 87, 50, 25, 10, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 190, 190, 87, 50, 50, 25, 25, 25, 25, 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: 880 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060977 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060977 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060977/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060977 Building REAL250005060978 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060978' /scratch/stefan/7916143/working/building/REAL250005060978 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060978 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060978/0 /scratch/stefan/7916143/working/building/REAL250005060978 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/86 `/scratch/stefan/7916143/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CC1) `REAL250005060978.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060978 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 33, 80, 107, 107, 107, 201, 201, 201, 37, 37, 37, 37, 12, 12, 4, 1, 80, 79, 107, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 769 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060978 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 73, 145, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 7, 1, 1, 1, 1, 79, 79, 79, 79, 145, 145, 201, 201, 31, 31, 7, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 851 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060978 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060978 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060978/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060978 Building REAL250005060979 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060979' /scratch/stefan/7916143/working/building/REAL250005060979 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060979 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060979/0 /scratch/stefan/7916143/working/building/REAL250005060979 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/87 `/scratch/stefan/7916143/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CCCO1) `REAL250005060979.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060979 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [16, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 16, 25, 41, 41, 41, 72, 72, 72, 72, 72, 16, 16, 16, 16, 10, 10, 4, 1, 25, 25, 41, 72, 72, 72, 72, 72, 72] 72 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 267 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060979 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [53, 41, 53, 66, 72, 72, 72, 72, 72, 72, 72, 72, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 66, 66, 72, 72, 41, 41, 12, 1, 1, 1, 1, 1, 1] 72 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 307 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060979 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060979 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060979/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060979 Building REAL250005060980 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060980' /scratch/stefan/7916143/working/building/REAL250005060980 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005060980 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060980/0 /scratch/stefan/7916143/working/building/REAL250005060980 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/88 `/scratch/stefan/7916143/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NNN=C1) `REAL250005060980.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060980 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NNN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 4, 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: [15, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 15, 29, 39, 39, 39, 57, 57, 57, 57, 15, 15, 15, 15, 9, 9, 4, 1, 29, 29, 39, 57, 57] 57 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060980 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NNN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 4, 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: [27, 16, 27, 48, 56, 56, 56, 57, 57, 57, 57, 57, 6, 6, 1, 6, 1, 1, 1, 1, 1, 27, 27, 27, 27, 48, 48, 56, 57, 16, 16, 6, 1, 1] 57 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060980 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005060980/1 /scratch/stefan/7916143/working/building/REAL250005060980 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/89 `/scratch/stefan/7916143/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CN=NN1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060980.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005060980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060980 none CC(CNC(=O)C1=CN=NN1)CNC(=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', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [60, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 60, 108, 147, 147, 147, 147, 147, 147, 147, 147, 62, 62, 62, 62, 29, 29, 7, 1, 1, 108, 108, 147, 147] 147 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 619 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060980 none CC(CNC(=O)C1=CN=NN1)CNC(=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', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [46, 23, 46, 94, 127, 127, 127, 147, 147, 147, 147, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 94, 94, 127, 147, 147, 23, 23, 4, 1] 147 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 560 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060980 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060980 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060980/0.* 1: /scratch/stefan/7916143/working/building/REAL250005060980/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060980 Building REAL250005060981 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060981' /scratch/stefan/7916143/working/building/REAL250005060981 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060981 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060981/0 /scratch/stefan/7916143/working/building/REAL250005060981 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/90 `/scratch/stefan/7916143/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1(C)CC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060981.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060981 none CC(CNC(=O)CC1(C)CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 75, 17, 17, 5, 17, 1, 1, 1, 1, 1, 126, 170, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127, 75, 75, 17, 5, 5, 2, 2, 2, 1, 1, 1, 1, 170, 169, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 898 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060981 none CC(CNC(=O)CC1(C)CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 62, 96, 96, 96, 196, 201, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 62, 61, 96, 196, 196, 201, 201, 201, 201, 201, 201, 201, 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: 858 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060981 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060981 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060981/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060981 Building REAL250005060982 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060982' /scratch/stefan/7916143/working/building/REAL250005060982 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060982 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060982/0 /scratch/stefan/7916143/working/building/REAL250005060982 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/91 `/scratch/stefan/7916143/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CN=CO1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060982.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060982 none CC(CNC(=O)C1=CN=CO1)CNC(=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', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 70, 143, 198, 198, 198, 201, 201, 201, 201, 201, 72, 72, 72, 72, 30, 30, 7, 1, 1, 143, 143, 198, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 844 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060982 none CC(CNC(=O)C1=CN=CO1)CNC(=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', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 66, 133, 185, 185, 185, 201, 201, 201, 201, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 132, 132, 185, 201, 201, 30, 30, 7, 1] 201 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 802 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060982 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060982 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060982/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060982 Building REAL250005060983 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060983' /scratch/stefan/7916143/working/building/REAL250005060983 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060983 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060983/0 /scratch/stefan/7916143/working/building/REAL250005060983 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/92 `/scratch/stefan/7916143/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060983.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060983 none C=CC(C)(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 119, 201, 201, 119, 119, 70, 32, 11, 30, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 70, 70, 32, 32, 32, 32, 11, 11, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 868 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060983 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060983 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060983/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060983 Building REAL250005060984 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060984' /scratch/stefan/7916143/working/building/REAL250005060984 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060984 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060984/0 /scratch/stefan/7916143/working/building/REAL250005060984 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/93 `/scratch/stefan/7916143/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1C) `REAL250005060984.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060984 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 31, 66, 101, 101, 101, 201, 201, 201, 201, 201, 31, 31, 31, 31, 11, 11, 3, 1, 66, 66, 101, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060984 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 92, 151, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 151, 150, 201, 201, 53, 53, 13, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 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, 35, 36, 37]) total number of confs: 856 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060984 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060984 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060984/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060984 Building REAL250005060985 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060985' /scratch/stefan/7916143/working/building/REAL250005060985 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060985 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060985/0 /scratch/stefan/7916143/working/building/REAL250005060985 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/94 `/scratch/stefan/7916143/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CCC1) `REAL250005060985.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060985 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 34, 71, 105, 105, 105, 201, 201, 201, 201, 35, 35, 35, 35, 15, 15, 4, 1, 71, 71, 105, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 738 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060985 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 71, 144, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 7, 1, 1, 1, 1, 1, 74, 74, 74, 74, 144, 144, 201, 201, 33, 33, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 851 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060985 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060985 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060985/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060985 Building REAL250005060986 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060986' /scratch/stefan/7916143/working/building/REAL250005060986 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060986 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060986/0 /scratch/stefan/7916143/working/building/REAL250005060986 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/95 `/scratch/stefan/7916143/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060986.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060986 none CCC(F)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 174, 139, 174, 139, 139, 70, 34, 12, 32, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 174, 139, 70, 70, 37, 37, 37, 37, 12, 12, 4, 1] 201 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 882 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060986 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060986 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060986/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060986 Building REAL250005060987 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060987' /scratch/stefan/7916143/working/building/REAL250005060987 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060987 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060987/0 /scratch/stefan/7916143/working/building/REAL250005060987 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/96 `/scratch/stefan/7916143/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCCF)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060987.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060987 none CC(CNC(=O)CCCF)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 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, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 25, 43, 77, 77, 77, 179, 198, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 43, 43, 77, 179, 179, 201, 201, 201, 201, 13, 13, 4, 1] 201 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 888 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060987 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060987 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060987/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060987 Building REAL250005060988 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060988' /scratch/stefan/7916143/working/building/REAL250005060988 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060988 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060988/0 /scratch/stefan/7916143/working/building/REAL250005060988 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/97 `/scratch/stefan/7916143/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1C[C@@H]1C) `REAL250005060988.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060988 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 31, 67, 102, 102, 102, 201, 201, 201, 201, 201, 31, 31, 31, 31, 12, 12, 4, 1, 67, 67, 102, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 720 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060988 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 54, 91, 150, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 149, 150, 201, 201, 54, 54, 13, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 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, 35, 36, 37]) total number of confs: 849 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060988 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060988 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060988/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060988 Building REAL250005060989 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060989' /scratch/stefan/7916143/working/building/REAL250005060989 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060989 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060989/0 /scratch/stefan/7916143/working/building/REAL250005060989 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/98 `/scratch/stefan/7916143/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060989.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060989 none C=CCCCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 165, 149, 44, 44, 44, 34, 26, 17, 26, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 199, 199, 183, 183, 149, 149, 44, 34, 34, 26, 26, 26, 26, 17, 17, 5, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1004 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060989 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060989 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060989/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060989 Building REAL250005060990 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060990' /scratch/stefan/7916143/working/building/REAL250005060990 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060990 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060990/0 /scratch/stefan/7916143/working/building/REAL250005060990 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/99 `/scratch/stefan/7916143/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060990.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060990 none CCC(C)(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [184, 193, 111, 193, 193, 111, 111, 65, 30, 12, 28, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 193, 193, 193, 193, 193, 111, 65, 65, 30, 30, 30, 30, 12, 12, 4, 1] 201 rigid atoms, others: [42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 998 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060990 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060990 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060990/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060990 Building REAL250005060991 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060991' /scratch/stefan/7916143/working/building/REAL250005060991 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060991 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060991/0 /scratch/stefan/7916143/working/building/REAL250005060991 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/100 `/scratch/stefan/7916143/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(N)=O)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060991.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060991 none CC(CNC(=O)C(N)=O)CNC(=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', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 11, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 6, 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: [64, 25, 66, 127, 193, 193, 193, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 127, 126, 193, 201, 201, 25, 25, 4, 1] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 796 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060991 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060991 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060991/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060991 Building REAL250005060992 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060992' /scratch/stefan/7916143/working/building/REAL250005060992 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060992 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060992/0 /scratch/stefan/7916143/working/building/REAL250005060992 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/101 `/scratch/stefan/7916143/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1CC1C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060992.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060992 none CC(CNC(=O)CC1CC1C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 111, 38, 38, 6, 38, 1, 1, 1, 1, 1, 143, 185, 201, 201, 201, 201, 201, 201, 201, 201, 143, 143, 143, 143, 111, 111, 38, 6, 6, 1, 1, 1, 1, 2, 2, 2, 185, 185, 201, 201] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 883 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060992 none CC(CNC(=O)CC1CC1C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 26, 48, 69, 69, 69, 168, 201, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 48, 48, 69, 168, 168, 201, 201, 201, 201, 201, 201, 201, 15, 15, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 826 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060992 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060992 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060992/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060992 Building REAL250005060993 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060993' /scratch/stefan/7916143/working/building/REAL250005060993 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060993 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060993/0 /scratch/stefan/7916143/working/building/REAL250005060993 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/102 `/scratch/stefan/7916143/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005060993.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060993 none CCC1(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 7, 7, 7, 38, 77, 77, 125, 185, 185, 185, 185, 185, 185, 185, 185, 1, 1, 3, 3, 3, 3, 3, 7, 38, 38, 77, 77, 77, 77, 125, 125, 185, 185, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 37, 38, 39, 40, 19, 20] 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, 35, 36]) total number of confs: 802 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060993 none CCC1(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 185, 82, 82, 82, 56, 28, 11, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 185, 185, 201, 201, 201, 201, 201, 82, 56, 56, 28, 28, 28, 28, 11, 11, 4, 1, 185, 185, 185, 185] 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: 742 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060993 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060993 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060993/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060993 Building REAL250005060994 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060994' /scratch/stefan/7916143/working/building/REAL250005060994 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060994 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060994/0 /scratch/stefan/7916143/working/building/REAL250005060994 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/103 `/scratch/stefan/7916143/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(CF)CC1) `REAL250005060994.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060994 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(CF)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 27, 67, 104, 104, 104, 193, 201, 193, 193, 27, 27, 27, 27, 11, 11, 4, 1, 67, 67, 104, 201, 201, 193, 193, 193, 193] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 745 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060994 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(CF)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 138, 192, 192, 192, 193, 193, 193, 193, 193, 7, 7, 1, 7, 1, 1, 9, 1, 1, 69, 69, 69, 69, 138, 137, 192, 193, 34, 34, 7, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 848 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060994 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060994 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060994/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060994 Building REAL250005060995 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060995' /scratch/stefan/7916143/working/building/REAL250005060995 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060995 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060995/0 /scratch/stefan/7916143/working/building/REAL250005060995 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/104 `/scratch/stefan/7916143/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)C) `REAL250005060995.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060995 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 63, 141, 198, 198, 198, 201, 201, 201, 68, 68, 68, 68, 25, 25, 7, 1, 139, 140, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 817 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060995 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060995 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060995/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060995 Building REAL250005060996 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060996' /scratch/stefan/7916143/working/building/REAL250005060996 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060996 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060996/0 /scratch/stefan/7916143/working/building/REAL250005060996 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/105 `/scratch/stefan/7916143/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C(C)C) `REAL250005060996.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060996 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 76, 132, 132, 132, 198, 198, 201, 201, 36, 36, 36, 36, 13, 13, 4, 1, 76, 76, 132, 198, 198, 198, 198, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 861 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060996 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060996 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060996/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060996 Building REAL250005060997 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060997' /scratch/stefan/7916143/working/building/REAL250005060997 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060997 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060997/0 /scratch/stefan/7916143/working/building/REAL250005060997 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/106 `/scratch/stefan/7916143/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H]1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005060997.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060997 none CC[C@@H]1C[C@H]1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 85, 85, 129, 180, 180, 180, 182, 182, 182, 182, 182, 3, 3, 3, 3, 3, 1, 1, 12, 53, 53, 85, 85, 85, 85, 129, 129, 180, 182] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060997 none CC[C@@H]1C[C@H]1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 182, 182, 182, 88, 182, 88, 88, 56, 26, 12, 26, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 182, 182, 88, 56, 56, 26, 26, 26, 26, 11, 11, 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: 752 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060997 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060997 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060997/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060997 Building REAL250005060998 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060998' /scratch/stefan/7916143/working/building/REAL250005060998 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060998 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060998/0 /scratch/stefan/7916143/working/building/REAL250005060998 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/107 `/scratch/stefan/7916143/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC12CC2) `REAL250005060998.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060998 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC12CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 31, 67, 108, 108, 108, 201, 201, 201, 201, 31, 31, 31, 31, 14, 14, 4, 1, 67, 67, 108, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060998 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC12CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 101, 163, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 11, 1, 1, 1, 1, 1, 102, 102, 102, 102, 162, 163, 201, 201, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 888 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060998 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060998 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060998/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060998 Building REAL250005060999 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005060999' /scratch/stefan/7916143/working/building/REAL250005060999 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005060999 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005060999/0 /scratch/stefan/7916143/working/building/REAL250005060999 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/108 `/scratch/stefan/7916143/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1CC(=O)N1) `REAL250005060999.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005060999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005060999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060999 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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: [42, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 43, 80, 124, 124, 124, 201, 201, 201, 201, 201, 44, 44, 44, 44, 21, 21, 7, 1, 80, 80, 124, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 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: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005060999 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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, 60, 106, 168, 200, 200, 200, 201, 201, 201, 201, 201, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 168, 167, 200, 201, 60, 60, 11, 1, 1, 1] 201 rigid atoms, others: [33, 34, 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]) total number of confs: 884 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005060999 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005060999 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005060999/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005060999 Building REAL250005061000 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061000' /scratch/stefan/7916143/working/building/REAL250005061000 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061000 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061000/0 /scratch/stefan/7916143/working/building/REAL250005061000 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/109 `/scratch/stefan/7916143/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CC(=O)N1) `REAL250005061000.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061000 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 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: [41, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 42, 80, 124, 124, 124, 185, 185, 185, 185, 185, 44, 44, 44, 44, 19, 19, 6, 1, 80, 80, 124, 185, 185, 185] 185 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 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: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061000 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 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: [109, 58, 107, 160, 185, 185, 185, 185, 185, 185, 185, 185, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 160, 159, 185, 185, 58, 58, 11, 1, 1, 1] 185 rigid atoms, others: [33, 34, 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]) total number of confs: 814 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061000 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061000 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061000/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061000 Building REAL250005061001 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061001' /scratch/stefan/7916143/working/building/REAL250005061001 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061001 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061001/0 /scratch/stefan/7916143/working/building/REAL250005061001 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/110 `/scratch/stefan/7916143/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005061001.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061001 none COC1(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 12, 12, 12, 52, 100, 103, 147, 198, 198, 198, 201, 201, 201, 201, 201, 1, 1, 5, 5, 5, 12, 52, 52, 104, 104, 104, 104, 147, 147, 198, 201, 1, 1, 1, 1] 201 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: 888 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061001 none COC1(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 134, 134, 134, 71, 30, 10, 27, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 134, 71, 71, 30, 30, 30, 30, 10, 10, 3, 1, 201, 201, 201, 201] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 757 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061001 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061001 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061001/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061001 Building REAL250005061002 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061002' /scratch/stefan/7916143/working/building/REAL250005061002 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061002 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061002/0 /scratch/stefan/7916143/working/building/REAL250005061002 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/111 `/scratch/stefan/7916143/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CSC1) `REAL250005061002.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061002 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CSC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 43, 91, 146, 146, 146, 201, 201, 201, 45, 45, 45, 45, 18, 18, 4, 1, 91, 90, 146, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 775 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061002 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CSC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 51, 100, 166, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 1, 10, 1, 1, 1, 1, 102, 102, 102, 102, 166, 166, 201, 201, 51, 51, 10, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 876 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061002 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061002 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061002/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061002 Building REAL250005061003 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061003' /scratch/stefan/7916143/working/building/REAL250005061003 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061003 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061003/0 /scratch/stefan/7916143/working/building/REAL250005061003 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/112 `/scratch/stefan/7916143/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061003.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061003 none C=CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 12, 28, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 121, 71, 71, 31, 31, 31, 31, 12, 12, 4, 1] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 876 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061003 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061003 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061003/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061003 Building REAL250005061004 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061004' /scratch/stefan/7916143/working/building/REAL250005061004 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061004 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061004/0 /scratch/stefan/7916143/working/building/REAL250005061004 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/113 `/scratch/stefan/7916143/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C[NH+](C)C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061004.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061004 none CC(CNC(=O)C[NH+](C)C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 8, 1, 11, 5, 9, 6, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 4, 7, 6, 7, 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 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 2 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: 5 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061004 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061004/1 /scratch/stefan/7916143/working/building/REAL250005061004 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/114 `/scratch/stefan/7916143/working/3D/114' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN(C)C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061004.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061004/1/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: REAL250005061004 none CC(CNC(=O)CN(C)C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 40, 59, 95, 95, 95, 189, 201, 201, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 59, 59, 95, 189, 189, 201, 201, 201, 201, 201, 201, 23, 23, 7, 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: 840 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061004 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061004 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061004/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061004/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061004 Building REAL250005061005 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061005' /scratch/stefan/7916143/working/building/REAL250005061005 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061005 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061005/0 /scratch/stefan/7916143/working/building/REAL250005061005 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/115 `/scratch/stefan/7916143/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061005.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061005 none C=CC(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 134, 201, 134, 134, 73, 35, 14, 35, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 134, 73, 73, 38, 38, 38, 38, 14, 14, 4, 1] 603 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061005 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061005 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061005/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061005 Building REAL250005061006 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061006' /scratch/stefan/7916143/working/building/REAL250005061006 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061006 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061006/0 /scratch/stefan/7916143/working/building/REAL250005061006 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/116 `/scratch/stefan/7916143/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1COC1) `REAL250005061006.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061006 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 44, 88, 136, 136, 136, 201, 201, 201, 45, 45, 45, 45, 18, 18, 4, 1, 87, 88, 136, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 757 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061006 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 49, 97, 163, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 1, 10, 1, 1, 1, 1, 100, 100, 100, 100, 161, 163, 201, 201, 49, 49, 10, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 881 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061006 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061006 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061006/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061006 Building REAL250005061007 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061007' /scratch/stefan/7916143/working/building/REAL250005061007 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061007 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061007/0 /scratch/stefan/7916143/working/building/REAL250005061007 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/117 `/scratch/stefan/7916143/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061007.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061007 none CO[C@H](C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 128, 201, 201, 128, 128, 72, 33, 13, 33, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 128, 72, 72, 35, 35, 35, 35, 13, 13, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 853 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061007 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061007 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061007/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061007 Building REAL250005061008 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061008' /scratch/stefan/7916143/working/building/REAL250005061008 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061008 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061008/0 /scratch/stefan/7916143/working/building/REAL250005061008 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/118 `/scratch/stefan/7916143/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061008.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061008 none CC=CC(O)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 12, 1, 11, 8, 5, 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, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 189, 127, 189, 127, 127, 66, 31, 11, 30, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 189, 567, 127, 66, 66, 34, 34, 34, 34, 11, 11, 3, 1] 603 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 1428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061008 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061008 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061008/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061008 Building REAL250005061009 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061009' /scratch/stefan/7916143/working/building/REAL250005061009 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061009 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061009/0 /scratch/stefan/7916143/working/building/REAL250005061009 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/119 `/scratch/stefan/7916143/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)[NH+](C)C) `REAL250005061009.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061009 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 5 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061009 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061009/1 /scratch/stefan/7916143/working/building/REAL250005061009 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/120 `/scratch/stefan/7916143/working/3D/120' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)N(C)C) `REAL250005061009.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061009/1/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: REAL250005061009 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 27, 42, 63, 63, 63, 99, 99, 99, 102, 102, 28, 28, 28, 28, 17, 17, 6, 1, 42, 42, 63, 99, 99, 99, 102, 102, 102, 102, 102, 102] 102 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 440 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061009 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061009 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061009/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061009/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061009 Building REAL250005061010 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061010' /scratch/stefan/7916143/working/building/REAL250005061010 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061010 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061010/0 /scratch/stefan/7916143/working/building/REAL250005061010 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/121 `/scratch/stefan/7916143/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(F)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061010.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061010 none CCC=C(F)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 141, 141, 120, 141, 120, 120, 76, 36, 12, 36, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 141, 120, 76, 76, 39, 39, 39, 39, 12, 12, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 907 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061010 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061010 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061010/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061010 Building REAL250005061011 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061011' /scratch/stefan/7916143/working/building/REAL250005061011 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061011 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061011/0 /scratch/stefan/7916143/working/building/REAL250005061011 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/122 `/scratch/stefan/7916143/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061011.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061011 none CCC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 139, 139, 92, 92, 92, 57, 24, 10, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 139, 139, 92, 57, 57, 24, 24, 24, 24, 10, 10, 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: 916 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061011 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061011 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061011/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061011 Building REAL250005061012 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061012' /scratch/stefan/7916143/working/building/REAL250005061012 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005061012 as failed and skipping /scratch/stefan/7916143/working /scratch/stefan/7916143 `/scratch/stefan/7916143/working/building/REAL250005061012' -> `/scratch/stefan/7916143/failed/REAL250005061012' Building REAL250005061013 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061013' /scratch/stefan/7916143/working/building/REAL250005061013 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061013 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061013/0 /scratch/stefan/7916143/working/building/REAL250005061013 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/123 `/scratch/stefan/7916143/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)CO) `REAL250005061013.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061013 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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, 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: [21, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 21, 36, 55, 55, 55, 85, 85, 85, 87, 21, 21, 21, 21, 9, 9, 3, 1, 36, 36, 55, 85, 85, 85, 85, 85, 85, 87, 87, 261] 261 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 644 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061013 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061013 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061013/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061013 Building REAL250005061014 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061014' /scratch/stefan/7916143/working/building/REAL250005061014 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061014 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061014/0 /scratch/stefan/7916143/working/building/REAL250005061014 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/124 `/scratch/stefan/7916143/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(F)CCC1) `REAL250005061014.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061014 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(F)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [25, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 25, 33, 49, 49, 49, 97, 97, 97, 97, 25, 25, 25, 25, 15, 15, 7, 1, 33, 33, 49, 97, 97, 97, 97, 97, 97] 97 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 337 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061014 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(F)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [68, 48, 68, 90, 95, 95, 95, 97, 97, 97, 97, 97, 13, 13, 1, 13, 1, 1, 1, 1, 1, 68, 68, 68, 68, 90, 90, 95, 97, 48, 48, 13, 1, 1, 1, 1, 1, 1] 97 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 423 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061014 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061014 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061014/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061014 Building REAL250005061015 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061015' /scratch/stefan/7916143/working/building/REAL250005061015 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061015 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061015/0 /scratch/stefan/7916143/working/building/REAL250005061015 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/125 `/scratch/stefan/7916143/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CO)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061015.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061015 none CC(CNC(=O)CO)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 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 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [27, 17, 27, 38, 51, 51, 51, 65, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 38, 38, 51, 65, 65, 195, 17, 17, 7, 1] 195 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: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061015 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061015 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061015/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061015 Building REAL250005061016 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061016' /scratch/stefan/7916143/working/building/REAL250005061016 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061016 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061016/0 /scratch/stefan/7916143/working/building/REAL250005061016 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/126 `/scratch/stefan/7916143/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CC(N)=O)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061016.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061016 none CC(CNC(=O)C=CC(N)=O)CNC(=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', 'C.2', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 12, 14, 14, 14, 20, 20, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 12, 12, 14, 20, 20, 21, 21, 7, 7, 2, 1] 21 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: 89 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061016 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061016 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061016/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061016 Building REAL250005061017 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061017' /scratch/stefan/7916143/working/building/REAL250005061017 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061017 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061017/0 /scratch/stefan/7916143/working/building/REAL250005061017 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/127 `/scratch/stefan/7916143/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061017.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061017 none CC(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 252 conformations in input total number of sets (complete confs): 252 using faster count positions algorithm for large data unique positions, atoms: [84, 63, 84, 63, 63, 42, 29, 19, 29, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 252, 63, 42, 42, 29, 29, 29, 29, 19, 19, 6, 1] 252 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: 605 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061017 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061017 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061017/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061017 Building REAL250005061018 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061018' /scratch/stefan/7916143/working/building/REAL250005061018 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061018 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061018/0 /scratch/stefan/7916143/working/building/REAL250005061018 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/128 `/scratch/stefan/7916143/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)CCC1) `REAL250005061018.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061018 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 336 conformations in input total number of sets (complete confs): 336 using faster count positions algorithm for large data unique positions, atoms: [24, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 23, 43, 66, 66, 66, 112, 112, 112, 112, 24, 24, 24, 24, 14, 14, 5, 1, 43, 43, 66, 336, 112, 112, 112, 112, 112, 112] 336 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 741 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061018 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 336 conformations in input total number of sets (complete confs): 336 using faster count positions algorithm for large data unique positions, atoms: [73, 44, 73, 99, 112, 112, 112, 112, 112, 112, 112, 112, 12, 12, 1, 12, 1, 1, 1, 1, 1, 73, 73, 73, 73, 99, 99, 112, 112, 44, 44, 12, 6, 1, 1, 1, 1, 1, 1] 336 rigid atoms, others: [33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 503 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061018 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061018 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061018/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061018 Building REAL250005061019 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061019' /scratch/stefan/7916143/working/building/REAL250005061019 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061019 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061019/0 /scratch/stefan/7916143/working/building/REAL250005061019 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/129 `/scratch/stefan/7916143/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(O)C1CC1) `REAL250005061019.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061019 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [12, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 16, 18, 18, 18, 37, 37, 42, 42, 12, 12, 12, 12, 10, 10, 6, 1, 16, 16, 18, 37, 111, 42, 42, 42, 42, 42] 126 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061019 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [36, 28, 36, 39, 40, 40, 40, 42, 42, 42, 42, 42, 19, 19, 6, 19, 1, 6, 1, 1, 1, 36, 36, 36, 36, 39, 39, 40, 42, 28, 28, 19, 6, 18, 1, 1, 1, 1, 1] 126 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: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061019 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061019 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061019/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061019 Building REAL250005061020 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061020' /scratch/stefan/7916143/working/building/REAL250005061020 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061020 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061020/0 /scratch/stefan/7916143/working/building/REAL250005061020 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/130 `/scratch/stefan/7916143/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061020.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061020 none C=CCC(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 162, 65, 162, 65, 65, 39, 21, 9, 21, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 162, 162, 162, 162, 65, 39, 39, 21, 21, 21, 21, 9, 9, 3, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 894 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061020 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061020 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061020/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061020 Building REAL250005061021 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061021' /scratch/stefan/7916143/working/building/REAL250005061021 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061021 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061021/0 /scratch/stefan/7916143/working/building/REAL250005061021 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/131 `/scratch/stefan/7916143/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1F) `REAL250005061021.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061021 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 34, 81, 137, 137, 137, 201, 201, 201, 34, 34, 34, 34, 14, 14, 4, 1, 81, 81, 137, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061021 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 115, 167, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 1, 13, 1, 1, 1, 1, 117, 117, 117, 117, 167, 166, 201, 201, 61, 61, 13, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 896 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061021 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061021 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061021/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061021 Building REAL250005061022 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061022' /scratch/stefan/7916143/working/building/REAL250005061022 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061022 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061022/0 /scratch/stefan/7916143/working/building/REAL250005061022 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/132 `/scratch/stefan/7916143/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)[NH+](C)C) `REAL250005061022.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061022 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 5 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061022 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061022/1 /scratch/stefan/7916143/working/building/REAL250005061022 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/133 `/scratch/stefan/7916143/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)N(C)C) `REAL250005061022.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061022/1/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: REAL250005061022 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 27, 42, 63, 63, 63, 99, 99, 99, 102, 102, 28, 28, 28, 28, 17, 17, 6, 1, 42, 42, 63, 99, 99, 99, 102, 102, 102, 102, 102, 102] 102 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 440 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061022 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061022 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061022/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061022/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061022 Building REAL250005061023 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061023' /scratch/stefan/7916143/working/building/REAL250005061023 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061023 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061023/0 /scratch/stefan/7916143/working/building/REAL250005061023 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/134 `/scratch/stefan/7916143/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCF)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061023.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061023 none CC(CNC(=O)CCF)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 78, 122, 122, 122, 193, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 78, 78, 122, 193, 193, 201, 201, 15, 15, 4, 1] 201 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 847 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061023 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061023 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061023/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061023 Building REAL250005061024 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061024' /scratch/stefan/7916143/working/building/REAL250005061024 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061024 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061024/0 /scratch/stefan/7916143/working/building/REAL250005061024 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/135 `/scratch/stefan/7916143/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)COC1) `REAL250005061024.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061024 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 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 312 conformations in input total number of sets (complete confs): 312 using faster count positions algorithm for large data unique positions, atoms: [29, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 28, 47, 71, 71, 71, 104, 104, 104, 104, 29, 29, 29, 29, 18, 18, 7, 1, 47, 47, 71, 312, 104, 104, 104, 104] 312 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 694 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061024 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 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 312 conformations in input total number of sets (complete confs): 312 using faster count positions algorithm for large data unique positions, atoms: [73, 44, 72, 91, 103, 103, 103, 104, 104, 104, 104, 104, 12, 12, 1, 12, 1, 1, 1, 1, 1, 73, 73, 73, 73, 90, 91, 103, 104, 44, 44, 12, 6, 1, 1, 1, 1] 312 rigid atoms, others: [33, 34, 35, 36, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 462 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061024 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061024 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061024/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061024 Building REAL250005061025 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061025' /scratch/stefan/7916143/working/building/REAL250005061025 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061025 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061025/0 /scratch/stefan/7916143/working/building/REAL250005061025 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/136 `/scratch/stefan/7916143/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1)=C1CC1) `REAL250005061025.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061025 none CC(C(=O)NCC(C)CNC(=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', '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', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 131, 74, 34, 16, 31, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 131, 74, 74, 34, 34, 34, 34, 16, 16, 4, 1, 201, 201, 201, 201] 201 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 727 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061025 none CC(C(=O)NCC(C)CNC(=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', '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', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 57, 100, 102, 160, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 12, 57, 57, 102, 102, 102, 102, 160, 160, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 18, 19, 20] set([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]) total number of confs: 904 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061025 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061025 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061025/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061025 Building REAL250005061026 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061026' /scratch/stefan/7916143/working/building/REAL250005061026 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061026 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061026/0 /scratch/stefan/7916143/working/building/REAL250005061026 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/137 `/scratch/stefan/7916143/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061026.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061026 none CCC1CC1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 12, 12, 12, 55, 89, 90, 132, 180, 180, 180, 184, 184, 184, 184, 184, 3, 3, 3, 3, 3, 1, 1, 1, 1, 12, 55, 55, 90, 90, 90, 90, 132, 132, 180, 184] 201 rigid atoms, others: [1, 2, 3, 4, 5, 26, 27, 28, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 771 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061026 none CCC1CC1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 184, 184, 184, 86, 86, 86, 52, 24, 12, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 184, 184, 184, 184, 86, 52, 52, 24, 24, 24, 24, 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: 738 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061026 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061026 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061026/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061026 Building REAL250005061027 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061027' /scratch/stefan/7916143/working/building/REAL250005061027 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061027 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061027/0 /scratch/stefan/7916143/working/building/REAL250005061027 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/138 `/scratch/stefan/7916143/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1(O)CC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061027.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061027 none CC(CNC(=O)CC1(O)CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [38, 33, 20, 20, 5, 20, 1, 1, 1, 1, 1, 38, 44, 46, 46, 46, 46, 46, 46, 46, 46, 38, 38, 38, 38, 33, 33, 20, 5, 5, 6, 1, 1, 1, 1, 44, 44, 46, 46] 138 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 189 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061027 none CC(CNC(=O)CC1(O)CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 14, 21, 28, 28, 28, 45, 46, 46, 46, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 21, 21, 28, 45, 45, 138, 46, 46, 46, 46, 10, 10, 4, 1] 138 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: 337 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061027 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061027 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061027/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061027 Building REAL250005061028 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061028' /scratch/stefan/7916143/working/building/REAL250005061028 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061028 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061028/0 /scratch/stefan/7916143/working/building/REAL250005061028 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/139 `/scratch/stefan/7916143/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CCF)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061028.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061028 none CC(CNC(=O)C=CCF)CNC(=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', 'C.2', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 30, 69, 119, 119, 118, 191, 191, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 68, 69, 119, 191, 191, 201, 201, 13, 13, 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: 790 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061028 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061028 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061028/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061028 Building REAL250005061029 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061029' /scratch/stefan/7916143/working/building/REAL250005061029 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061029 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061029/0 /scratch/stefan/7916143/working/building/REAL250005061029 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/140 `/scratch/stefan/7916143/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061029.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061029 none C#CCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 193, 101, 101, 101, 58, 28, 10, 27, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 193, 193, 101, 58, 58, 29, 29, 29, 29, 10, 10, 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: 870 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061029 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061029 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061029/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061029 Building REAL250005061030 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061030' /scratch/stefan/7916143/working/building/REAL250005061030 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061030 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061030/0 /scratch/stefan/7916143/working/building/REAL250005061030 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/141 `/scratch/stefan/7916143/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN1CCC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061030.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061030 none CC(CNC(=O)CN1CCC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 109, 41, 41, 6, 41, 1, 1, 1, 1, 1, 153, 183, 198, 198, 198, 201, 201, 201, 201, 201, 157, 157, 157, 157, 109, 109, 41, 6, 6, 1, 1, 1, 1, 1, 1, 183, 181, 198, 201] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39]) total number of confs: 870 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061030 none CC(CNC(=O)CN1CCC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 33, 58, 99, 99, 99, 179, 201, 201, 201, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 58, 57, 99, 179, 179, 201, 201, 201, 201, 201, 201, 22, 22, 7, 1] 201 rigid atoms, others: [39, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 818 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061030 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061030/1 /scratch/stefan/7916143/working/building/REAL250005061030 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/142 `/scratch/stefan/7916143/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C[NH+]1CCC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061030.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061030 none CC(CNC(=O)C[NH+]1CCC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 5 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061030 none CC(CNC(=O)C[NH+]1CCC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 1] 5 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: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061030 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061030 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061030/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061030/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061030 Building REAL250005061031 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061031' /scratch/stefan/7916143/working/building/REAL250005061031 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061031 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061031/0 /scratch/stefan/7916143/working/building/REAL250005061031 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/143 `/scratch/stefan/7916143/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#C[C@H]1C[C@H]1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061031.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061031 none C#C[C@H]1C[C@H]1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 39, 84, 84, 147, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 7, 39, 39, 86, 86, 86, 86, 147, 147, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061031 none C#C[C@H]1C[C@H]1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 145, 201, 145, 145, 88, 37, 16, 34, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 145, 88, 88, 37, 37, 37, 37, 16, 16, 4, 1] 201 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 777 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061031 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061031 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061031/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061031 Building REAL250005061032 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061032' /scratch/stefan/7916143/working/building/REAL250005061032 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061032 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061032/0 /scratch/stefan/7916143/working/building/REAL250005061032 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/144 `/scratch/stefan/7916143/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1C2CCC21) `REAL250005061032.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061032 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1C2CCC21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 43, 103, 160, 160, 160, 201, 201, 201, 201, 45, 45, 45, 45, 19, 19, 4, 1, 103, 102, 160, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 784 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061032 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1C2CCC21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 77, 147, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 1, 10, 1, 1, 1, 1, 1, 80, 80, 80, 80, 146, 147, 201, 201, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 845 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061032 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061032 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061032/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061032 Building REAL250005061033 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061033' /scratch/stefan/7916143/working/building/REAL250005061033 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061033 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061033/0 /scratch/stefan/7916143/working/building/REAL250005061033 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/145 `/scratch/stefan/7916143/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061033.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061033 none C=C1CCC1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 52, 104, 104, 151, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 10, 52, 52, 105, 105, 105, 105, 151, 151, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 22, 23, 24, 25, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 879 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061033 none C=C1CCC1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 128, 128, 128, 71, 33, 12, 31, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 128, 71, 71, 34, 34, 34, 34, 12, 12, 4, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 736 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061033 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061033 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061033/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061033 Building REAL250005061034 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061034' /scratch/stefan/7916143/working/building/REAL250005061034 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061034 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061034/0 /scratch/stefan/7916143/working/building/REAL250005061034 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/146 `/scratch/stefan/7916143/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1[C@H](C)[C@@H]1C) `REAL250005061034.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061034 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1[C@H](C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 71, 107, 107, 107, 201, 201, 201, 201, 201, 201, 32, 32, 32, 32, 12, 12, 2, 1, 71, 71, 107, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 727 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061034 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1[C@H](C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 52, 91, 157, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 157, 157, 201, 201, 52, 52, 11, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 883 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061034 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061034 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061034/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061034 Building REAL250005061035 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061035' /scratch/stefan/7916143/working/building/REAL250005061035 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061035 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061035/0 /scratch/stefan/7916143/working/building/REAL250005061035 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/147 `/scratch/stefan/7916143/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H](C)[NH+](C)C) `REAL250005061035.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061035 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H](C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 5 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061035 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061035/1 /scratch/stefan/7916143/working/building/REAL250005061035 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/148 `/scratch/stefan/7916143/working/3D/148' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H](C)N(C)C) `REAL250005061035.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061035/1/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: REAL250005061035 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H](C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 28, 42, 63, 63, 63, 97, 97, 97, 102, 102, 29, 29, 29, 29, 18, 18, 7, 1, 42, 42, 63, 97, 97, 97, 102, 102, 102, 102, 102, 102] 102 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 429 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061035 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061035 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061035/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061035/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061035 Building REAL250005061036 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061036' /scratch/stefan/7916143/working/building/REAL250005061036 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061036 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061036/0 /scratch/stefan/7916143/working/building/REAL250005061036 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/149 `/scratch/stefan/7916143/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061036.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061036 none CC=CC=CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 200, 157, 157, 157, 114, 46, 18, 46, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 157, 113, 114, 50, 50, 50, 50, 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: 802 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061036 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061036 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061036/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061036 Building REAL250005061037 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061037' /scratch/stefan/7916143/working/building/REAL250005061037 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061037 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061037/0 /scratch/stefan/7916143/working/building/REAL250005061037 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/150 `/scratch/stefan/7916143/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061037.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061037 none COCC=CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 132, 99, 99, 59, 59, 59, 48, 37, 22, 38, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 135, 135, 135, 132, 132, 99, 99, 59, 48, 48, 38, 38, 38, 38, 22, 22, 6, 1] 135 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: 589 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061037 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061037 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061037/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061037 Building REAL250005061038 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061038' /scratch/stefan/7916143/working/building/REAL250005061038 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061038 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061038/0 /scratch/stefan/7916143/working/building/REAL250005061038 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/151 `/scratch/stefan/7916143/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)COC1) `REAL250005061038.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061038 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 38, 81, 110, 110, 110, 201, 201, 201, 201, 40, 40, 40, 40, 16, 16, 4, 1, 81, 81, 110, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 727 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061038 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 32, 75, 161, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 6, 1, 1, 1, 1, 1, 79, 79, 79, 79, 161, 161, 201, 201, 32, 32, 6, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 874 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061038 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061038 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061038/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061038 Building REAL250005061039 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061039' /scratch/stefan/7916143/working/building/REAL250005061039 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061039 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061039/0 /scratch/stefan/7916143/working/building/REAL250005061039 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/152 `/scratch/stefan/7916143/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCO1) `REAL250005061039.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061039 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [34, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 34, 51, 76, 76, 76, 112, 112, 112, 35, 35, 35, 35, 19, 19, 5, 1, 51, 51, 76, 112, 112, 112, 112, 112] 112 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 427 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061039 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [71, 47, 70, 102, 112, 112, 112, 112, 112, 112, 112, 112, 11, 11, 1, 11, 1, 1, 1, 1, 71, 71, 71, 71, 101, 102, 112, 112, 47, 47, 11, 1, 1, 1, 1, 1] 112 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 487 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061039 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061039 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061039/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061039 Building REAL250005061040 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061040' /scratch/stefan/7916143/working/building/REAL250005061040 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061040 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061040/0 /scratch/stefan/7916143/working/building/REAL250005061040 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/153 `/scratch/stefan/7916143/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCN=[N+]=[N-])CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061040.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061040 none CC(CNC(=O)CCN=[N+]=[N-])CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 8, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 39, 62, 62, 62, 153, 174, 201, 201, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 39, 39, 62, 153, 153, 174, 174, 8, 8, 3, 1] 201 rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 794 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061040 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061040 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061040/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061040 Building REAL250005061041 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061041' /scratch/stefan/7916143/working/building/REAL250005061041 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061041 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061041/0 /scratch/stefan/7916143/working/building/REAL250005061041 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/154 `/scratch/stefan/7916143/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061041.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061041 none C#CCOCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 142, 87, 87, 87, 60, 28, 10, 24, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 142, 142, 87, 60, 60, 28, 28, 28, 28, 10, 10, 3, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 998 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061041 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061041 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061041/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061041 Building REAL250005061042 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061042' /scratch/stefan/7916143/working/building/REAL250005061042 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061042 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061042/0 /scratch/stefan/7916143/working/building/REAL250005061042 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/155 `/scratch/stefan/7916143/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)O) `REAL250005061042.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061042 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 23, 33, 52, 52, 52, 86, 86, 86, 23, 23, 23, 23, 15, 15, 5, 1, 33, 33, 52, 86, 86, 86, 86, 86, 86, 258] 258 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 615 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061042 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061042 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061042/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061042 Building REAL250005061043 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061043' /scratch/stefan/7916143/working/building/REAL250005061043 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061043 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061043/0 /scratch/stefan/7916143/working/building/REAL250005061043 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/156 `/scratch/stefan/7916143/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061043.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061043 none CC1=CC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 68, 117, 118, 168, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 13, 68, 68, 118, 118, 118, 118, 168, 168, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 881 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061043 none CC1=CC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 106, 106, 106, 61, 28, 11, 26, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 106, 61, 61, 29, 29, 29, 29, 11, 11, 3, 1] 201 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 727 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061043 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061043 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061043/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061043 Building REAL250005061044 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061044' /scratch/stefan/7916143/working/building/REAL250005061044 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061044 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061044/0 /scratch/stefan/7916143/working/building/REAL250005061044 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/157 `/scratch/stefan/7916143/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(=O)N(C)C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061044.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061044 none CC(CNC(=O)C(=O)N(C)C)CNC(=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, 6, 7, 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 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, 11, 13, 13, 13, 19, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 11, 11, 13, 19, 19, 19, 19, 19, 19, 8, 8, 5, 1] 19 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: 71 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061044 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061044 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061044/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061044 Building REAL250005061045 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061045' /scratch/stefan/7916143/working/building/REAL250005061045 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061045 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061045/0 /scratch/stefan/7916143/working/building/REAL250005061045 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/158 `/scratch/stefan/7916143/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061045.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061045 none CSC=CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 182, 113, 113, 113, 65, 29, 11, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 182, 182, 113, 65, 65, 29, 29, 29, 29, 11, 11, 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: 713 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061045 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061045 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061045/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061045 Building REAL250005061046 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061046' /scratch/stefan/7916143/working/building/REAL250005061046 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061046 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061046/0 /scratch/stefan/7916143/working/building/REAL250005061046 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/159 `/scratch/stefan/7916143/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061046.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061046 none CCC(C)(O)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [199, 186, 114, 186, 186, 114, 114, 63, 31, 13, 29, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 186, 186, 186, 558, 114, 63, 63, 32, 32, 32, 32, 13, 13, 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: 1466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061046 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061046 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061046/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061046 Building REAL250005061047 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061047' /scratch/stefan/7916143/working/building/REAL250005061047 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005061047 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061047/0 /scratch/stefan/7916143/working/building/REAL250005061047 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/160 `/scratch/stefan/7916143/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061047.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061047 none CC[N@H+](C)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 64, 55, 64, 64, 28, 28, 28, 16, 15, 12, 15, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 64, 64, 64, 55, 55, 28, 16, 16, 15, 15, 15, 15, 12, 12, 7, 1] 67 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: 309 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061047 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061047/1 /scratch/stefan/7916143/working/building/REAL250005061047 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/161 `/scratch/stefan/7916143/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061047.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061047/1/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: REAL250005061047 none CC[N@@H+](C)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 64, 56, 64, 64, 28, 28, 28, 16, 15, 12, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 64, 64, 64, 56, 56, 28, 16, 16, 15, 15, 15, 15, 12, 12, 7, 1] 67 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: 305 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061047 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `2' /scratch/stefan/7916143/working/building/REAL250005061047/2 /scratch/stefan/7916143/working/building/REAL250005061047 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 2 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/162 `/scratch/stefan/7916143/working/3D/162' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061047.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005061047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061047/2/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: REAL250005061047 none CCN(C)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 186, 198, 101, 101, 101, 56, 23, 9, 23, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 198, 198, 198, 186, 186, 101, 56, 56, 24, 24, 24, 24, 9, 9, 3, 1] 201 rigid atoms, others: [41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 882 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061047 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061047 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061047/0.* 2: /scratch/stefan/7916143/working/building/REAL250005061047/2.* 1: /scratch/stefan/7916143/working/building/REAL250005061047/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061047 Building REAL250005061048 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061048' /scratch/stefan/7916143/working/building/REAL250005061048 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061048 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061048/0 /scratch/stefan/7916143/working/building/REAL250005061048 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/163 `/scratch/stefan/7916143/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061048.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061048 none C=C1CC(C(=O)NCC(C)CNC(=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', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 9, 47, 77, 80, 140, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 9, 47, 47, 80, 80, 80, 80, 140, 140, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 20, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 868 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061048 none C=C1CC(C(=O)NCC(C)CNC(=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', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 125, 125, 84, 46, 21, 41, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 125, 84, 84, 46, 46, 46, 46, 21, 21, 4, 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: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061048 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061048 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061048/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061048 Building REAL250005061049 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061049' /scratch/stefan/7916143/working/building/REAL250005061049 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061049 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061049/0 /scratch/stefan/7916143/working/building/REAL250005061049 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/164 `/scratch/stefan/7916143/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCC1F) `REAL250005061049.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061049 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 90, 145, 145, 145, 201, 201, 201, 201, 40, 40, 40, 40, 16, 16, 4, 1, 89, 90, 145, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 772 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061049 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 56, 100, 158, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 11, 1, 1, 1, 1, 1, 103, 103, 103, 103, 158, 158, 201, 201, 56, 56, 11, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 876 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061049 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061049 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061049/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061049 Building REAL250005061050 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061050' /scratch/stefan/7916143/working/building/REAL250005061050 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061050 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061050/0 /scratch/stefan/7916143/working/building/REAL250005061050 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/165 `/scratch/stefan/7916143/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CN=CN1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061050.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061050 none CC(CNC(=O)C1=CN=CN1)CNC(=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', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [69, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 69, 135, 183, 183, 183, 187, 187, 187, 187, 187, 72, 72, 72, 72, 31, 31, 7, 1, 1, 1, 135, 134, 183, 187] 187 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 783 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061050 none CC(CNC(=O)C1=CN=CN1)CNC(=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', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [44, 22, 44, 103, 159, 159, 159, 187, 187, 187, 187, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 101, 103, 159, 187, 187, 187, 22, 22, 8, 1] 187 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: 683 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061050 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061050 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061050/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061050 Building REAL250005061051 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061051' /scratch/stefan/7916143/working/building/REAL250005061051 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061051 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061051/0 /scratch/stefan/7916143/working/building/REAL250005061051 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/166 `/scratch/stefan/7916143/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCCO1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061051.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061051 none CC(CNC(=O)C1=CCCO1)CNC(=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', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 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, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 7, 7, 1, 7, 1, 1, 1, 1, 1, 80, 152, 199, 199, 199, 201, 201, 201, 201, 201, 83, 83, 83, 83, 34, 34, 8, 1, 1, 1, 1, 1, 152, 151, 199, 201] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 852 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061051 none CC(CNC(=O)C1=CCCO1)CNC(=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', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 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, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 64, 128, 184, 184, 184, 201, 201, 201, 201, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 127, 128, 184, 201, 201, 201, 201, 201, 29, 29, 8, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 768 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061051 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061051 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061051/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061051 Building REAL250005061052 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061052' /scratch/stefan/7916143/working/building/REAL250005061052 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061052 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061052/0 /scratch/stefan/7916143/working/building/REAL250005061052 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/167 `/scratch/stefan/7916143/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061052.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061052 none CCC[C@H](O)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 157, 105, 157, 157, 105, 105, 53, 25, 10, 25, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 471, 105, 53, 53, 26, 26, 26, 26, 10, 10, 3, 1] 603 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061052 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061052 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061052/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061052 Building REAL250005061053 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061053' /scratch/stefan/7916143/working/building/REAL250005061053 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061053 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061053/0 /scratch/stefan/7916143/working/building/REAL250005061053 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/168 `/scratch/stefan/7916143/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061053.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061053 none CC(C)[C@H](O)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 201, 127, 186, 186, 127, 127, 66, 31, 11, 29, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 558, 127, 66, 66, 32, 32, 32, 32, 11, 11, 4, 1] 603 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1416 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061053 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061053 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061053/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061053 Building REAL250005061054 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061054' /scratch/stefan/7916143/working/building/REAL250005061054 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061054 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061054/0 /scratch/stefan/7916143/working/building/REAL250005061054 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/169 `/scratch/stefan/7916143/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061054.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061054 none CCOC=CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 124, 124, 105, 105, 105, 83, 53, 23, 52, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 134, 134, 134, 134, 134, 124, 124, 105, 82, 83, 54, 54, 54, 54, 23, 23, 5, 1] 134 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: 519 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061054 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061054 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061054/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061054 Building REAL250005061055 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061055' /scratch/stefan/7916143/working/building/REAL250005061055 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061055 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061055/0 /scratch/stefan/7916143/working/building/REAL250005061055 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/170 `/scratch/stefan/7916143/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H](C)O) `REAL250005061055.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061055 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 264 conformations in input total number of sets (complete confs): 264 using faster count positions algorithm for large data unique positions, atoms: [34, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 34, 42, 61, 61, 61, 88, 88, 88, 34, 34, 34, 34, 21, 21, 8, 1, 42, 42, 61, 88, 88, 88, 264] 264 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 640 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061055 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061055 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061055/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061055 Building REAL250005061056 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061056' /scratch/stefan/7916143/working/building/REAL250005061056 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061056 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061056/0 /scratch/stefan/7916143/working/building/REAL250005061056 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/171 `/scratch/stefan/7916143/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CCO)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061056.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061056 none CC(CNC(=O)C=CCO)CNC(=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', 'C.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 4, 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: [24, 9, 26, 65, 118, 118, 118, 194, 194, 201, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 65, 65, 118, 194, 194, 201, 201, 603, 9, 9, 3, 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: 1363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061056 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061056 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061056/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061056 Building REAL250005061057 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061057' /scratch/stefan/7916143/working/building/REAL250005061057 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061057 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061057/0 /scratch/stefan/7916143/working/building/REAL250005061057 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/172 `/scratch/stefan/7916143/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061057.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061057 none COC(C)(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 136, 200, 200, 136, 136, 72, 37, 16, 37, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 200, 200, 200, 200, 200, 136, 72, 72, 39, 39, 39, 39, 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: 843 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061057 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061057 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061057/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061057 Building REAL250005061058 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061058' /scratch/stefan/7916143/working/building/REAL250005061058 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061058 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061058/0 /scratch/stefan/7916143/working/building/REAL250005061058 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/173 `/scratch/stefan/7916143/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCCCO)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061058.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061058 none CC(CNC(=O)CCCCO)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 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, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 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: [22, 14, 22, 36, 59, 59, 59, 153, 179, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 36, 36, 59, 153, 153, 192, 192, 197, 199, 201, 201, 603, 14, 14, 4, 1] 603 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1554 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061058 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061058 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061058/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061058 Building REAL250005061059 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061059' /scratch/stefan/7916143/working/building/REAL250005061059 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061059 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061059/0 /scratch/stefan/7916143/working/building/REAL250005061059 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/174 `/scratch/stefan/7916143/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(CO)CC1) `REAL250005061059.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061059 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [27, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 29, 61, 111, 111, 111, 192, 201, 192, 192, 29, 29, 29, 29, 12, 12, 4, 1, 61, 61, 111, 201, 201, 603, 192, 192, 192, 192] 603 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1343 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061059 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [61, 30, 60, 133, 191, 191, 191, 192, 192, 192, 192, 192, 7, 7, 1, 7, 1, 1, 8, 1, 1, 61, 61, 61, 61, 133, 133, 191, 192, 30, 30, 7, 8, 8, 24, 1, 1, 1, 1] 603 rigid atoms, others: [35, 36, 37, 38, 14, 16, 17, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 856 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061059 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061059 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061059/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061059 Building REAL250005061060 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061060' /scratch/stefan/7916143/working/building/REAL250005061060 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061060 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061060/0 /scratch/stefan/7916143/working/building/REAL250005061060 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/175 `/scratch/stefan/7916143/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(F)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061060.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061060 none COC(F)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 107, 197, 107, 107, 64, 35, 13, 33, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 197, 107, 64, 64, 36, 36, 36, 36, 13, 13, 4, 1] 201 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 859 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061060 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061060 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061060/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061060 Building REAL250005061061 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061061' /scratch/stefan/7916143/working/building/REAL250005061061 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061061 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061061/0 /scratch/stefan/7916143/working/building/REAL250005061061 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/176 `/scratch/stefan/7916143/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C12CC1CC2) `REAL250005061061.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061061 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C12CC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 36, 72, 99, 99, 99, 201, 201, 201, 201, 37, 37, 37, 37, 16, 16, 4, 1, 72, 72, 99, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 569 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061061 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C12CC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 78, 150, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 7, 1, 1, 1, 1, 1, 80, 80, 80, 80, 150, 150, 201, 201, 33, 33, 7, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 855 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061061 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061061 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061061/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061061 Building REAL250005061062 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061062' /scratch/stefan/7916143/working/building/REAL250005061062 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061062 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061062/0 /scratch/stefan/7916143/working/building/REAL250005061062 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/177 `/scratch/stefan/7916143/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@H](C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061062.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061062 none C=C[C@H](C)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 173, 201, 201, 81, 81, 81, 46, 23, 11, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 173, 173, 81, 46, 46, 24, 24, 24, 24, 11, 11, 4, 1] 201 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 902 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061062 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061062 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061062/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061062 Building REAL250005061063 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061063' /scratch/stefan/7916143/working/building/REAL250005061063 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061063 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061063/0 /scratch/stefan/7916143/working/building/REAL250005061063 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/178 `/scratch/stefan/7916143/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CC1CC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061063.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061063 none CC(CNC(=O)C=CC1CC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 90, 37, 37, 9, 36, 9, 1, 1, 1, 1, 124, 176, 201, 201, 201, 201, 201, 201, 201, 201, 124, 124, 124, 124, 90, 90, 37, 9, 9, 1, 1, 1, 1, 1, 176, 176, 201, 201] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 850 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061063 none CC(CNC(=O)C=CC1CC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 24, 57, 98, 98, 98, 153, 153, 201, 201, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 56, 57, 98, 153, 153, 201, 201, 201, 201, 201, 9, 9, 3, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 767 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061063 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061063 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061063/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061063 Building REAL250005061064 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061064' /scratch/stefan/7916143/working/building/REAL250005061064 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061064 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061064/0 /scratch/stefan/7916143/working/building/REAL250005061064 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/179 `/scratch/stefan/7916143/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(CC)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061064.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061064 none CC=C(CC)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 88, 158, 201, 88, 88, 59, 24, 10, 23, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 201, 201, 201, 201, 201, 88, 59, 59, 24, 24, 24, 24, 10, 10, 3, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 841 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061064 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061064 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061064/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061064 Building REAL250005061065 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061065' /scratch/stefan/7916143/working/building/REAL250005061065 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061065 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061065/0 /scratch/stefan/7916143/working/building/REAL250005061065 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/180 `/scratch/stefan/7916143/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061065.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061065 none C=CC(C)(O)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 1, 11, 8, 5, 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, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 140, 201, 201, 140, 140, 73, 32, 13, 32, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 140, 73, 73, 34, 34, 34, 34, 13, 13, 4, 1] 603 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 1457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061065 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061065 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061065/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061065 Building REAL250005061066 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061066' /scratch/stefan/7916143/working/building/REAL250005061066 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061066 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061066/0 /scratch/stefan/7916143/working/building/REAL250005061066 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/181 `/scratch/stefan/7916143/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061066.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061066 none CC(CNC(=O)C1=CCC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [63, 27, 6, 6, 1, 6, 1, 1, 1, 1, 64, 128, 167, 167, 167, 174, 174, 174, 174, 174, 66, 66, 66, 66, 27, 27, 6, 1, 1, 1, 1, 1, 127, 128, 167, 174] 174 rigid atoms, others: [4, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 710 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061066 none CC(CNC(=O)C1=CCC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [74, 38, 77, 144, 174, 174, 174, 174, 174, 174, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 144, 143, 174, 174, 174, 174, 174, 174, 38, 38, 10, 1] 174 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: 743 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061066 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061066 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061066/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061066 Building REAL250005061067 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061067' /scratch/stefan/7916143/working/building/REAL250005061067 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061067 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061067/0 /scratch/stefan/7916143/working/building/REAL250005061067 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/182 `/scratch/stefan/7916143/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061067.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061067 none CON=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 138, 138, 79, 38, 16, 36, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 138, 79, 79, 41, 41, 41, 41, 16, 16, 4, 1] 201 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 788 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061067 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061067 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061067/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061067 Building REAL250005061068 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061068' /scratch/stefan/7916143/working/building/REAL250005061068 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061068 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061068/0 /scratch/stefan/7916143/working/building/REAL250005061068 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/183 `/scratch/stefan/7916143/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(F)CC1) `REAL250005061068.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061068 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 80, 137, 137, 137, 201, 201, 201, 40, 40, 40, 40, 18, 18, 4, 1, 80, 80, 137, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061068 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 58, 112, 164, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 11, 1, 1, 1, 1, 118, 118, 118, 118, 164, 163, 201, 201, 58, 58, 11, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 896 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061068 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061068 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061068/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061068 Building REAL250005061069 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061069' /scratch/stefan/7916143/working/building/REAL250005061069 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061069 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061069/0 /scratch/stefan/7916143/working/building/REAL250005061069 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/184 `/scratch/stefan/7916143/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NOCC1) `REAL250005061069.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061069 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 11, 13, 13, 13, 21, 21, 21, 21, 7, 7, 7, 7, 5, 5, 3, 1, 11, 11, 13, 21, 21, 21, 21] 21 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061069 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 16, 18, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 16, 16, 16, 16, 18, 18, 21, 21, 12, 12, 8, 1, 1, 1, 1] 21 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061069 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061069 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061069/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061069 Building REAL250005061070 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061070' /scratch/stefan/7916143/working/building/REAL250005061070 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061070 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061070/0 /scratch/stefan/7916143/working/building/REAL250005061070 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/185 `/scratch/stefan/7916143/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC(C)(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061070.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061070 none C#CC(C)(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 132, 201, 201, 132, 132, 84, 37, 19, 36, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 132, 84, 84, 39, 39, 39, 39, 19, 19, 4, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 911 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061070 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061070 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061070/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061070 Building REAL250005061071 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061071' /scratch/stefan/7916143/working/building/REAL250005061071 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061071 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061071/0 /scratch/stefan/7916143/working/building/REAL250005061071 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/186 `/scratch/stefan/7916143/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)COC1CC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061071.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061071 none CC(CNC(=O)COC1CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 156, 85, 85, 21, 85, 6, 1, 1, 1, 1, 171, 192, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 171, 171, 156, 156, 85, 21, 21, 1, 1, 1, 1, 1, 192, 192, 201, 201] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 802 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061071 none CC(CNC(=O)COC1CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 17, 27, 42, 42, 42, 144, 181, 201, 201, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 27, 27, 42, 144, 144, 201, 201, 201, 201, 201, 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: 721 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061071 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061071 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061071/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061071 Building REAL250005061072 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061072' /scratch/stefan/7916143/working/building/REAL250005061072 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061072 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061072/0 /scratch/stefan/7916143/working/building/REAL250005061072 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/187 `/scratch/stefan/7916143/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NC=CN1) `REAL250005061072.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061072 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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: [17, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 25, 26, 26, 26, 27, 27, 27, 27, 17, 17, 17, 17, 14, 14, 6, 1, 25, 25, 26, 27, 27, 27] 27 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061072 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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: [29, 14, 29, 44, 51, 51, 51, 51, 51, 51, 51, 51, 6, 6, 1, 6, 1, 1, 1, 1, 1, 29, 29, 29, 29, 44, 44, 51, 51, 14, 14, 6, 1, 1, 1] 51 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 225 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061072 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061072 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061072/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061072 Building REAL250005061073 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061073' /scratch/stefan/7916143/working/building/REAL250005061073 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061073 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061073/0 /scratch/stefan/7916143/working/building/REAL250005061073 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/188 `/scratch/stefan/7916143/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061073.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061073 none CCCC=CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 151, 151, 87, 87, 87, 71, 40, 22, 45, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 151, 151, 87, 71, 71, 45, 45, 45, 45, 22, 22, 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: 890 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061073 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061073 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061073/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061073 Building REAL250005061074 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061074' /scratch/stefan/7916143/working/building/REAL250005061074 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061074 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061074/0 /scratch/stefan/7916143/working/building/REAL250005061074 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/189 `/scratch/stefan/7916143/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061074.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061074 none CC=C(F)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 163, 200, 163, 163, 104, 52, 23, 52, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 163, 104, 104, 55, 55, 55, 55, 23, 23, 5, 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: 788 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061074 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061074 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061074/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061074 Building REAL250005061075 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061075' /scratch/stefan/7916143/working/building/REAL250005061075 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061075 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061075/0 /scratch/stefan/7916143/working/building/REAL250005061075 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/190 `/scratch/stefan/7916143/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CO)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061075.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061075 none CCC(CO)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 50, 35, 50, 52, 35, 35, 19, 12, 7, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 50, 52, 52, 156, 35, 19, 19, 12, 12, 12, 12, 7, 7, 2, 1] 159 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: 390 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061075 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061075 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061075/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061075 Building REAL250005061076 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061076' /scratch/stefan/7916143/working/building/REAL250005061076 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061076 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061076/0 /scratch/stefan/7916143/working/building/REAL250005061076 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/191 `/scratch/stefan/7916143/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)CO) `REAL250005061076.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061076 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [13, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 21, 32, 32, 32, 59, 59, 61, 13, 13, 13, 13, 8, 8, 2, 1, 21, 21, 32, 59, 59, 59, 59, 61, 61, 183] 183 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 452 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061076 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061076 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061076/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061076 Building REAL250005061077 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061077' /scratch/stefan/7916143/working/building/REAL250005061077 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061077 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061077/0 /scratch/stefan/7916143/working/building/REAL250005061077 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/192 `/scratch/stefan/7916143/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CON=C1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061077.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061077 none CC(CNC(=O)C1=CON=C1)CNC(=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', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 5, 5, 1, 5, 1, 1, 1, 1, 1, 78, 148, 201, 201, 201, 201, 201, 201, 201, 201, 81, 81, 81, 81, 31, 31, 5, 1, 1, 148, 148, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 866 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061077 none CC(CNC(=O)C1=CON=C1)CNC(=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', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 41, 88, 120, 120, 120, 201, 201, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 88, 87, 120, 201, 201, 17, 17, 4, 1] 201 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 657 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061077 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061077 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061077/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061077 Building REAL250005061078 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061078' /scratch/stefan/7916143/working/building/REAL250005061078 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061078 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061078/0 /scratch/stefan/7916143/working/building/REAL250005061078 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/193 `/scratch/stefan/7916143/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1CF) `REAL250005061078.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061078 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1CF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 28, 52, 84, 84, 84, 197, 197, 197, 197, 197, 201, 28, 28, 28, 28, 11, 11, 4, 1, 52, 52, 84, 197, 197, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 681 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061078 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1CF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 56, 98, 166, 194, 194, 194, 197, 197, 197, 197, 197, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 10, 102, 102, 102, 102, 166, 164, 194, 197, 56, 56, 13, 1, 1, 10, 10] 201 rigid atoms, others: [34, 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, 36, 37]) total number of confs: 917 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061078 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061078 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061078/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061078 Building REAL250005061079 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061079' /scratch/stefan/7916143/working/building/REAL250005061079 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061079 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061079/0 /scratch/stefan/7916143/working/building/REAL250005061079 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/194 `/scratch/stefan/7916143/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005061079.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061079 none C#CC1(C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 36, 78, 77, 143, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 6, 36, 36, 80, 80, 80, 80, 142, 143, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 36, 35, 33, 34, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 859 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061079 none C#CC1(C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 128, 128, 128, 76, 31, 13, 31, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 128, 76, 76, 32, 32, 32, 32, 13, 13, 4, 1, 201, 201, 201, 201] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 740 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061079 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061079 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061079/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061079 Building REAL250005061080 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061080' /scratch/stefan/7916143/working/building/REAL250005061080 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061080 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061080/0 /scratch/stefan/7916143/working/building/REAL250005061080 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/195 `/scratch/stefan/7916143/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=COCC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061080.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061080 none CC(CNC(=O)C1=COCC1)CNC(=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', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 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, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 9, 9, 1, 9, 1, 1, 1, 1, 1, 89, 156, 200, 200, 200, 201, 201, 201, 201, 201, 92, 92, 92, 92, 41, 41, 9, 1, 1, 1, 1, 1, 156, 156, 200, 201] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 883 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061080 none CC(CNC(=O)C1=COCC1)CNC(=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', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 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, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 41, 96, 156, 156, 156, 201, 201, 201, 201, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 96, 95, 156, 201, 201, 201, 201, 201, 20, 20, 6, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 697 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061080 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061080 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061080/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061080 Building REAL250005061081 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061081' /scratch/stefan/7916143/working/building/REAL250005061081 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061081 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061081/0 /scratch/stefan/7916143/working/building/REAL250005061081 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/196 `/scratch/stefan/7916143/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)O) `REAL250005061081.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061081 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 264 conformations in input total number of sets (complete confs): 264 using faster count positions algorithm for large data unique positions, atoms: [33, 22, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 33, 41, 60, 60, 60, 88, 88, 88, 33, 33, 33, 33, 22, 22, 8, 1, 41, 41, 60, 88, 88, 88, 264] 264 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 634 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061081 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061081 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061081/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061081 Building REAL250005061082 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061082' /scratch/stefan/7916143/working/building/REAL250005061082 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061082 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061082/0 /scratch/stefan/7916143/working/building/REAL250005061082 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/197 `/scratch/stefan/7916143/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1C=CCC1) `REAL250005061082.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061082 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 34, 71, 105, 105, 105, 201, 201, 201, 201, 34, 34, 34, 34, 14, 14, 4, 1, 71, 71, 105, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 699 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061082 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 87, 153, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 1, 10, 1, 1, 1, 1, 1, 88, 88, 88, 88, 153, 153, 201, 201, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 871 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061082 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061082 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061082/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061082 Building REAL250005061083 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061083' /scratch/stefan/7916143/working/building/REAL250005061083 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061083 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061083/0 /scratch/stefan/7916143/working/building/REAL250005061083 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/198 `/scratch/stefan/7916143/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C(C)O) `REAL250005061083.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061083 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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, 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: [35, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 38, 80, 123, 123, 123, 186, 186, 200, 201, 38, 38, 38, 38, 15, 15, 4, 1, 80, 80, 123, 186, 186, 186, 186, 201, 201, 201, 201, 603] 603 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1477 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061083 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061083 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061083/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061083 Building REAL250005061084 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061084' /scratch/stefan/7916143/working/building/REAL250005061084 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061084 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061084/0 /scratch/stefan/7916143/working/building/REAL250005061084 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/199 `/scratch/stefan/7916143/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061084.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061084 none C=C1CC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 65, 116, 116, 166, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 13, 65, 65, 116, 116, 116, 116, 166, 166, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 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]) total number of confs: 905 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061084 none C=C1CC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 111, 111, 68, 33, 15, 29, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 111, 68, 68, 33, 33, 33, 33, 15, 15, 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: 714 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061084 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061084 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061084/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061084 Building REAL250005061085 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061085' /scratch/stefan/7916143/working/building/REAL250005061085 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061085 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061085/0 /scratch/stefan/7916143/working/building/REAL250005061085 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/200 `/scratch/stefan/7916143/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)CF) `REAL250005061085.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061085 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)CF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 69, 109, 109, 109, 199, 199, 201, 35, 35, 35, 35, 13, 13, 4, 1, 69, 69, 109, 199, 199, 199, 199, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 844 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061085 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061085 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061085/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061085 Building REAL250005061086 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061086' /scratch/stefan/7916143/working/building/REAL250005061086 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061086 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061086/0 /scratch/stefan/7916143/working/building/REAL250005061086 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/201 `/scratch/stefan/7916143/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061086.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061086 none C=C(C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 108, 108, 61, 27, 11, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 108, 61, 61, 28, 28, 28, 28, 11, 11, 4, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 828 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061086 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061086 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061086/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061086 Building REAL250005061087 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061087' /scratch/stefan/7916143/working/building/REAL250005061087 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061087 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061087/0 /scratch/stefan/7916143/working/building/REAL250005061087 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/202 `/scratch/stefan/7916143/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061087.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061087 none CC(C)=C(C)C(=O)NCC(C)CNC(=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 160, 201, 160, 160, 97, 50, 20, 48, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 160, 97, 97, 51, 51, 51, 51, 20, 20, 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: 789 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061087 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061087 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061087/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061087 Building REAL250005061088 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061088' /scratch/stefan/7916143/working/building/REAL250005061088 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061088 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061088/0 /scratch/stefan/7916143/working/building/REAL250005061088 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/203 `/scratch/stefan/7916143/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061088.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061088 none CCCC(O)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 154, 97, 154, 97, 97, 52, 27, 10, 26, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 154, 462, 97, 52, 52, 27, 27, 27, 27, 10, 10, 3, 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: 1370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061088 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061088 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061088/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061088 Building REAL250005061089 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061089' /scratch/stefan/7916143/working/building/REAL250005061089 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061089 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061089/0 /scratch/stefan/7916143/working/building/REAL250005061089 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/204 `/scratch/stefan/7916143/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061089.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061089 none CCC(O)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 177, 200, 89, 89, 89, 48, 22, 9, 21, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 600, 177, 177, 89, 48, 48, 23, 23, 23, 23, 9, 9, 3, 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: 1491 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061089 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061089 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061089/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061089 Building REAL250005061090 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061090' /scratch/stefan/7916143/working/building/REAL250005061090 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061090 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061090/0 /scratch/stefan/7916143/working/building/REAL250005061090 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/205 `/scratch/stefan/7916143/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061090.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061090 none CC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 158, 158, 109, 53, 23, 50, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 158, 109, 109, 55, 55, 55, 55, 23, 23, 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: 834 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061090 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061090 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061090/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061090 Building REAL250005061091 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061091' /scratch/stefan/7916143/working/building/REAL250005061091 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061091 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061091/0 /scratch/stefan/7916143/working/building/REAL250005061091 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/206 `/scratch/stefan/7916143/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CC1F) `REAL250005061091.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061091 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 86, 115, 115, 115, 201, 201, 201, 201, 42, 42, 42, 42, 16, 16, 4, 1, 86, 86, 115, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 746 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061091 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 73, 142, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 6, 1, 1, 1, 1, 1, 76, 76, 76, 76, 142, 141, 201, 201, 31, 31, 6, 2, 2, 2, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 851 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061091 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061091 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061091/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061091 Building REAL250005061092 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061092' /scratch/stefan/7916143/working/building/REAL250005061092 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061092 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061092/0 /scratch/stefan/7916143/working/building/REAL250005061092 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/207 `/scratch/stefan/7916143/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1C[C@@H](O)C1) `REAL250005061092.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061092 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1C[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [30, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 33, 75, 122, 122, 122, 201, 201, 201, 201, 201, 201, 33, 33, 33, 33, 14, 14, 5, 1, 75, 75, 122, 201, 201, 603, 201, 201] 603 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 1341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061092 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1C[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [92, 45, 93, 156, 200, 200, 200, 201, 201, 201, 201, 201, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 156, 156, 200, 201, 45, 45, 10, 1, 1, 3, 1, 1] 603 rigid atoms, others: [34, 35, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 879 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061092 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061092 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061092/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061092 Building REAL250005061093 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061093' /scratch/stefan/7916143/working/building/REAL250005061093 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061093 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061093/0 /scratch/stefan/7916143/working/building/REAL250005061093 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/208 `/scratch/stefan/7916143/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1C) `REAL250005061093.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061093 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 31, 66, 101, 101, 101, 201, 201, 201, 201, 201, 31, 31, 31, 31, 11, 11, 3, 1, 66, 66, 101, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061093 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 92, 151, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 151, 150, 201, 201, 53, 53, 13, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 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, 35, 36, 37]) total number of confs: 856 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061093 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061093 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061093/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061093 Building REAL250005061094 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061094' /scratch/stefan/7916143/working/building/REAL250005061094 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061094 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061094/0 /scratch/stefan/7916143/working/building/REAL250005061094 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/209 `/scratch/stefan/7916143/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061094.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061094 none CNC(=O)CC(=O)NCC(C)CNC(=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 182, 201, 103, 103, 103, 55, 29, 13, 28, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 182, 182, 103, 55, 55, 29, 29, 29, 29, 13, 13, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 838 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061094 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061094 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061094/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061094 Building REAL250005061095 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061095' /scratch/stefan/7916143/working/building/REAL250005061095 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061095 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061095/0 /scratch/stefan/7916143/working/building/REAL250005061095 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/210 `/scratch/stefan/7916143/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC=CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061095.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061095 none C=CC=CCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 191, 106, 106, 106, 73, 39, 21, 44, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 191, 106, 73, 73, 44, 44, 44, 44, 21, 21, 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: 913 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061095 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061095 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061095/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061095 Building REAL250005061096 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061096' /scratch/stefan/7916143/working/building/REAL250005061096 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061096 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061096/0 /scratch/stefan/7916143/working/building/REAL250005061096 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/211 `/scratch/stefan/7916143/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCC(N)=O)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061096.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061096 none CC(CNC(=O)CCC(N)=O)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 11, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 15, 22, 35, 53, 53, 53, 116, 124, 125, 125, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 35, 35, 53, 116, 116, 124, 124, 125, 125, 15, 15, 4, 1] 125 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: 546 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061096 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061096 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061096/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061096 Building REAL250005061097 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061097' /scratch/stefan/7916143/working/building/REAL250005061097 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061097 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061097/0 /scratch/stefan/7916143/working/building/REAL250005061097 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/212 `/scratch/stefan/7916143/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061097.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061097 none CC(O)CCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 194, 201, 177, 98, 98, 98, 52, 27, 10, 27, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 196, 196, 177, 177, 98, 52, 52, 29, 29, 29, 29, 10, 10, 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: 1490 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061097 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061097 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061097/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061097 Building REAL250005061098 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061098' /scratch/stefan/7916143/working/building/REAL250005061098 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061098 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061098/0 /scratch/stefan/7916143/working/building/REAL250005061098 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/213 `/scratch/stefan/7916143/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061098.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061098 none C#CCC(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 96, 170, 96, 96, 50, 24, 10, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 170, 170, 170, 170, 96, 50, 50, 25, 25, 25, 25, 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: 921 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061098 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061098 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061098/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061098 Building REAL250005061099 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061099' /scratch/stefan/7916143/working/building/REAL250005061099 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061099 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061099/0 /scratch/stefan/7916143/working/building/REAL250005061099 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/214 `/scratch/stefan/7916143/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)CCO) `REAL250005061099.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061099 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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, 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: [31, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 31, 61, 103, 103, 103, 191, 191, 201, 201, 32, 32, 32, 32, 15, 15, 4, 1, 60, 61, 103, 191, 191, 191, 191, 201, 201, 201, 201, 603] 603 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1475 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061099 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061099 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061099/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061099 Building REAL250005061100 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061100' /scratch/stefan/7916143/working/building/REAL250005061100 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061100 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061100/0 /scratch/stefan/7916143/working/building/REAL250005061100 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/215 `/scratch/stefan/7916143/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](O)CF) `REAL250005061100.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061100 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](O)CF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 12, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 4, 7, 7, 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: [34, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 34, 46, 70, 70, 70, 137, 137, 137, 140, 34, 34, 34, 34, 21, 21, 7, 1, 46, 46, 70, 411, 140, 140] 420 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 1007 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061100 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061100 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061100/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061100 Building REAL250005061101 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061101' /scratch/stefan/7916143/working/building/REAL250005061101 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061101 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061101/0 /scratch/stefan/7916143/working/building/REAL250005061101 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/216 `/scratch/stefan/7916143/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)CC1) `REAL250005061101.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061101 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [35, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 38, 87, 141, 141, 141, 201, 201, 201, 39, 39, 39, 39, 18, 18, 4, 1, 87, 87, 141, 603, 201, 201, 201, 201] 603 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061101 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [107, 57, 105, 164, 201, 201, 201, 201, 201, 201, 201, 201, 12, 12, 1, 12, 1, 1, 1, 1, 108, 108, 108, 108, 164, 163, 201, 201, 57, 57, 12, 6, 1, 1, 1, 1] 603 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 902 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061101 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061101 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061101/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061101 Building REAL250005061102 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061102' /scratch/stefan/7916143/working/building/REAL250005061102 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061102 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061102/0 /scratch/stefan/7916143/working/building/REAL250005061102 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/217 `/scratch/stefan/7916143/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1CC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061102.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061102 none CC(CNC(=O)CC1CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 84, 23, 23, 3, 23, 1, 1, 1, 1, 125, 169, 201, 201, 201, 201, 201, 201, 201, 201, 125, 125, 125, 125, 84, 84, 23, 3, 3, 1, 1, 1, 1, 1, 169, 169, 201, 201] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061102 none CC(CNC(=O)CC1CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 27, 60, 83, 83, 83, 162, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 60, 60, 83, 162, 162, 201, 201, 201, 201, 201, 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: 893 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061102 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061102 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061102/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061102 Building REAL250005061103 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061103' /scratch/stefan/7916143/working/building/REAL250005061103 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061103 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061103/0 /scratch/stefan/7916143/working/building/REAL250005061103 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/218 `/scratch/stefan/7916143/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)F) `REAL250005061103.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061103 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 14, 21, 21, 21, 44, 44, 44, 11, 11, 11, 11, 9, 9, 4, 1, 14, 14, 21, 44, 44, 44, 44, 44, 44] 44 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061103 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061103 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061103/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061103 Building REAL250005061104 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061104' /scratch/stefan/7916143/working/building/REAL250005061104 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061104 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061104/0 /scratch/stefan/7916143/working/building/REAL250005061104 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/219 `/scratch/stefan/7916143/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(F)F) `REAL250005061104.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061104 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 20, 20, 20, 7, 7, 7, 7, 5, 5, 4, 1, 7, 7, 9, 20, 20, 20] 20 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061104 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061104 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061104/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061104 Building REAL250005061105 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061105' /scratch/stefan/7916143/working/building/REAL250005061105 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061105 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061105/0 /scratch/stefan/7916143/working/building/REAL250005061105 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/220 `/scratch/stefan/7916143/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061105.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061105 none COCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 135, 135, 135, 67, 32, 11, 32, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 135, 67, 67, 34, 34, 34, 34, 11, 11, 3, 1] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 844 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061105 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061105 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061105/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061105 Building REAL250005061106 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061106' /scratch/stefan/7916143/working/building/REAL250005061106 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061106 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061106/0 /scratch/stefan/7916143/working/building/REAL250005061106 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/221 `/scratch/stefan/7916143/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061106.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061106 none CCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 102, 102, 102, 61, 31, 12, 28, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 191, 102, 61, 61, 31, 31, 31, 31, 12, 12, 4, 1] 201 rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 872 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061106 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061106 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061106/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061106 Building REAL250005061107 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061107' /scratch/stefan/7916143/working/building/REAL250005061107 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061107 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061107/0 /scratch/stefan/7916143/working/building/REAL250005061107 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/222 `/scratch/stefan/7916143/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=CO1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061107.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061107 none CC(CNC(=O)C1=CC=CO1)CNC(=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', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 6, 6, 1, 6, 1, 1, 1, 1, 1, 77, 150, 200, 200, 200, 201, 201, 201, 201, 201, 79, 79, 79, 79, 30, 30, 7, 1, 1, 1, 150, 150, 200, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 849 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061107 none CC(CNC(=O)C1=CC=CO1)CNC(=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', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 64, 130, 180, 180, 180, 201, 201, 201, 201, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 128, 129, 180, 201, 201, 201, 28, 28, 7, 1] 201 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 773 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061107 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061107 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061107/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061107 Building REAL250005061108 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061108' /scratch/stefan/7916143/working/building/REAL250005061108 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061108 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061108/0 /scratch/stefan/7916143/working/building/REAL250005061108 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/223 `/scratch/stefan/7916143/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061108.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061108 none CC(=O)NCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 201, 198, 107, 107, 107, 59, 27, 10, 24, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 198, 198, 107, 59, 59, 27, 27, 27, 27, 10, 10, 3, 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: 840 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061108 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061108 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061108/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061108 Building REAL250005061109 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061109' /scratch/stefan/7916143/working/building/REAL250005061109 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061109 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061109/0 /scratch/stefan/7916143/working/building/REAL250005061109 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/224 `/scratch/stefan/7916143/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061109.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061109 none CC(C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 201, 201, 128, 128, 128, 74, 37, 14, 34, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 74, 74, 37, 37, 37, 37, 14, 14, 4, 1] 201 rigid atoms, others: [39, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 866 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061109 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061109 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061109/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061109 Building REAL250005061110 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061110' /scratch/stefan/7916143/working/building/REAL250005061110 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061110 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061110/0 /scratch/stefan/7916143/working/building/REAL250005061110 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/225 `/scratch/stefan/7916143/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1C) `REAL250005061110.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061110 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 33, 68, 102, 102, 102, 201, 201, 201, 33, 33, 33, 33, 13, 13, 4, 1, 68, 68, 102, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061110 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 52, 90, 152, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 1, 13, 1, 1, 1, 1, 91, 91, 91, 91, 152, 151, 201, 201, 52, 52, 13, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 852 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061110 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061110 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061110/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061110 Building REAL250005061111 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061111' /scratch/stefan/7916143/working/building/REAL250005061111 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061111 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061111/0 /scratch/stefan/7916143/working/building/REAL250005061111 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/226 `/scratch/stefan/7916143/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061111.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061111 none CCOCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 201, 197, 95, 95, 95, 50, 26, 11, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 197, 95, 50, 50, 26, 26, 26, 26, 11, 11, 4, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 862 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061111 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061111 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061111/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061111 Building REAL250005061112 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061112' /scratch/stefan/7916143/working/building/REAL250005061112 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061112 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061112/0 /scratch/stefan/7916143/working/building/REAL250005061112 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/227 `/scratch/stefan/7916143/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061112.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061112 none CC(C)=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 158, 158, 158, 104, 50, 20, 48, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 158, 104, 104, 51, 51, 51, 51, 20, 20, 4, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 794 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061112 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061112 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061112/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061112 Building REAL250005061113 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061113' /scratch/stefan/7916143/working/building/REAL250005061113 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061113 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061113/0 /scratch/stefan/7916143/working/building/REAL250005061113 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/228 `/scratch/stefan/7916143/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCCO1) `REAL250005061113.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061113 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [21, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 21, 32, 46, 46, 46, 82, 82, 82, 82, 21, 21, 21, 21, 15, 15, 5, 1, 32, 32, 46, 82, 82, 82, 82, 82, 82, 82] 82 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 292 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061113 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [60, 44, 59, 77, 82, 82, 82, 82, 82, 82, 82, 82, 12, 12, 1, 12, 1, 1, 1, 1, 1, 60, 60, 60, 60, 77, 77, 82, 82, 44, 44, 12, 1, 1, 1, 1, 1, 1, 1] 82 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 370 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061113 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061113 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061113/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061113 Building REAL250005061114 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061114' /scratch/stefan/7916143/working/building/REAL250005061114 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061114 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061114/0 /scratch/stefan/7916143/working/building/REAL250005061114 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/229 `/scratch/stefan/7916143/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061114.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061114 none CSCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 124, 124, 124, 65, 29, 11, 28, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 189, 189, 124, 65, 65, 30, 30, 30, 30, 11, 11, 3, 1] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 805 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061114 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061114 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061114/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061114 Building REAL250005061115 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061115' /scratch/stefan/7916143/working/building/REAL250005061115 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061115 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061115/0 /scratch/stefan/7916143/working/building/REAL250005061115 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/230 `/scratch/stefan/7916143/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061115.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061115 none CC(C)CCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 199, 201, 187, 79, 79, 79, 45, 22, 9, 22, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 200, 201, 201, 201, 201, 199, 199, 187, 187, 79, 45, 45, 22, 22, 22, 22, 9, 9, 3, 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: 882 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061115 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061115 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061115/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061115 Building REAL250005061116 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061116' /scratch/stefan/7916143/working/building/REAL250005061116 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061116 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061116/0 /scratch/stefan/7916143/working/building/REAL250005061116 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/231 `/scratch/stefan/7916143/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=CN1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061116.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061116 none CC(CNC(=O)C1=CC=CN1)CNC(=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', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 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: [77, 33, 7, 7, 1, 7, 1, 1, 1, 1, 1, 77, 149, 200, 200, 200, 201, 201, 201, 201, 201, 80, 80, 80, 80, 33, 33, 7, 1, 1, 1, 1, 149, 148, 200, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 838 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061116 none CC(CNC(=O)C1=CC=CN1)CNC(=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', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 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: [55, 26, 55, 118, 173, 173, 173, 201, 201, 201, 201, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 116, 118, 173, 201, 201, 201, 201, 26, 26, 6, 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: 746 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061116 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061116 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061116/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061116 Building REAL250005061117 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061117' /scratch/stefan/7916143/working/building/REAL250005061117 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061117 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061117/0 /scratch/stefan/7916143/working/building/REAL250005061117 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/232 `/scratch/stefan/7916143/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=COC=C1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061117.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061117 none CC(CNC(=O)C1=COC=C1)CNC(=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', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 5, 5, 1, 5, 1, 1, 1, 1, 1, 83, 157, 200, 200, 200, 201, 201, 201, 201, 201, 85, 85, 85, 85, 30, 30, 5, 1, 1, 1, 156, 157, 200, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061117 none CC(CNC(=O)C1=COC=C1)CNC(=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', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 41, 91, 140, 140, 140, 201, 201, 201, 201, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 91, 91, 140, 201, 201, 201, 19, 19, 5, 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: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061117 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061117 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061117/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061117 Building REAL250005061118 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061118' /scratch/stefan/7916143/working/building/REAL250005061118 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061118 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061118/0 /scratch/stefan/7916143/working/building/REAL250005061118 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/233 `/scratch/stefan/7916143/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061118.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061118 none CCCCCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 198, 189, 92, 92, 92, 68, 37, 18, 37, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 198, 198, 189, 189, 92, 68, 67, 39, 39, 39, 39, 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: 895 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061118 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061118 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061118/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061118 Building REAL250005061119 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061119' /scratch/stefan/7916143/working/building/REAL250005061119 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061119 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061119/0 /scratch/stefan/7916143/working/building/REAL250005061119 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/234 `/scratch/stefan/7916143/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC(C)(C)C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061119.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061119 none CC(CNC(=O)CC(C)(C)C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 46, 103, 157, 157, 157, 199, 201, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 102, 103, 157, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 19, 19, 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: 873 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061119 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061119 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061119/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061119 Building REAL250005061120 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061120' /scratch/stefan/7916143/working/building/REAL250005061120 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061120 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061120/0 /scratch/stefan/7916143/working/building/REAL250005061120 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/235 `/scratch/stefan/7916143/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061120.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061120 none CCCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 199, 187, 78, 78, 78, 45, 22, 10, 22, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 200, 201, 201, 201, 201, 199, 199, 187, 187, 78, 45, 45, 22, 22, 22, 22, 10, 10, 3, 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: 862 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061120 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061120 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061120/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061120 Building REAL250005061121 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061121' /scratch/stefan/7916143/working/building/REAL250005061121 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061121 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061121/0 /scratch/stefan/7916143/working/building/REAL250005061121 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/236 `/scratch/stefan/7916143/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061121.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061121 none CC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 134, 201, 134, 134, 95, 42, 18, 40, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 134, 94, 95, 43, 43, 43, 43, 18, 18, 4, 1] 201 rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 898 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061121 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061121 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061121/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061121 Building REAL250005061122 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061122' /scratch/stefan/7916143/working/building/REAL250005061122 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061122 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061122/0 /scratch/stefan/7916143/working/building/REAL250005061122 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/237 `/scratch/stefan/7916143/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061122.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061122 none CCC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 114, 192, 114, 114, 62, 31, 13, 29, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 192, 192, 192, 192, 114, 62, 62, 32, 32, 32, 32, 13, 13, 3, 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: 868 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061122 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061122 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061122/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061122 Building REAL250005061123 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061123' /scratch/stefan/7916143/working/building/REAL250005061123 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061123 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061123/0 /scratch/stefan/7916143/working/building/REAL250005061123 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/238 `/scratch/stefan/7916143/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061123.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061123 none CCC(CC)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 170, 133, 170, 196, 133, 133, 67, 32, 13, 30, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 170, 196, 196, 196, 196, 196, 133, 67, 67, 32, 32, 32, 32, 13, 13, 4, 1] 201 rigid atoms, others: [42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1008 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061123 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061123 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061123/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061123 Building REAL250005061124 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061124' /scratch/stefan/7916143/working/building/REAL250005061124 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061124 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061124/0 /scratch/stefan/7916143/working/building/REAL250005061124 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/239 `/scratch/stefan/7916143/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=NN1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061124.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061124 none CC(CNC(=O)C1=CC=NN1)CNC(=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', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [72, 33, 8, 8, 1, 8, 1, 1, 1, 1, 1, 71, 135, 185, 185, 185, 188, 188, 188, 188, 188, 75, 75, 75, 75, 33, 33, 8, 1, 1, 1, 135, 135, 185, 188] 188 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 784 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061124 none CC(CNC(=O)C1=CC=NN1)CNC(=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', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [60, 30, 61, 127, 166, 166, 166, 188, 188, 188, 188, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 125, 126, 166, 188, 188, 188, 30, 30, 9, 1] 188 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: 727 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061124 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061124 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061124/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061124 Building REAL250005061125 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061125' /scratch/stefan/7916143/working/building/REAL250005061125 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061125 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061125/0 /scratch/stefan/7916143/working/building/REAL250005061125 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/240 `/scratch/stefan/7916143/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061125.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061125 none CCOC(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 112, 199, 112, 112, 62, 28, 11, 27, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 199, 199, 199, 199, 112, 62, 62, 29, 29, 29, 29, 11, 11, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 844 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061125 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061125 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061125/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061125 Building REAL250005061126 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061126' /scratch/stefan/7916143/working/building/REAL250005061126 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061126 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061126/0 /scratch/stefan/7916143/working/building/REAL250005061126 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/241 `/scratch/stefan/7916143/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CNN=C1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061126.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061126 none CC(CNC(=O)C1=CNN=C1)CNC(=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', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [40, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 39, 74, 108, 108, 108, 109, 109, 109, 109, 109, 41, 41, 41, 41, 17, 17, 4, 1, 1, 1, 74, 74, 108, 109] 109 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061126 none CC(CNC(=O)C1=CNN=C1)CNC(=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', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 19, 43, 89, 115, 115, 115, 115, 115, 115, 115, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 89, 88, 115, 115, 115, 115, 19, 19, 6, 1] 115 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: 463 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061126 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061126 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061126/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061126 Building REAL250005061127 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061127' /scratch/stefan/7916143/working/building/REAL250005061127 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061127 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061127/0 /scratch/stefan/7916143/working/building/REAL250005061127 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/242 `/scratch/stefan/7916143/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061127.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061127 none COCCCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 159, 160, 66, 66, 66, 40, 30, 19, 30, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 194, 176, 176, 160, 160, 66, 40, 40, 30, 30, 30, 30, 19, 19, 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: 980 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061127 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061127 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061127/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061127 Building REAL250005061128 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061128' /scratch/stefan/7916143/working/building/REAL250005061128 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061128 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061128/0 /scratch/stefan/7916143/working/building/REAL250005061128 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/243 `/scratch/stefan/7916143/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NOC=C1) `REAL250005061128.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061128 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NOC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [24, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 24, 43, 57, 57, 57, 73, 73, 73, 73, 24, 24, 24, 24, 13, 13, 6, 1, 43, 43, 57, 73, 73] 73 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061128 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NOC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [40, 20, 40, 60, 72, 72, 72, 73, 73, 73, 73, 73, 7, 7, 1, 7, 1, 1, 1, 1, 1, 40, 40, 40, 40, 60, 60, 72, 73, 20, 20, 7, 1, 1] 73 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061128 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061128 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061128/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061128 Building REAL250005061129 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061129' /scratch/stefan/7916143/working/building/REAL250005061129 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061129 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061129/0 /scratch/stefan/7916143/working/building/REAL250005061129 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/244 `/scratch/stefan/7916143/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061129.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061129 none CCC=C(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 198, 97, 198, 97, 97, 61, 25, 11, 23, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 198, 198, 198, 198, 97, 61, 61, 26, 26, 26, 26, 11, 11, 3, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 708 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061129 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061129 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061129/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061129 Building REAL250005061130 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061130' /scratch/stefan/7916143/working/building/REAL250005061130 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061130 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061130/0 /scratch/stefan/7916143/working/building/REAL250005061130 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/245 `/scratch/stefan/7916143/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061130.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061130 none COC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 132, 199, 132, 132, 74, 37, 15, 37, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 199, 199, 199, 199, 132, 74, 74, 39, 39, 39, 39, 15, 15, 4, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 831 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061130 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061130 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061130/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061130 Building REAL250005061131 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061131' /scratch/stefan/7916143/working/building/REAL250005061131 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061131 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061131/0 /scratch/stefan/7916143/working/building/REAL250005061131 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/246 `/scratch/stefan/7916143/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061131.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061131 none CC(C)OCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 201, 154, 86, 86, 86, 44, 20, 8, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 154, 154, 86, 44, 44, 20, 20, 20, 20, 8, 8, 2, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 838 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061131 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061131 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061131/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061131 Building REAL250005061132 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061132' /scratch/stefan/7916143/working/building/REAL250005061132 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061132 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061132/0 /scratch/stefan/7916143/working/building/REAL250005061132 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/247 `/scratch/stefan/7916143/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061132.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061132 none CCCOCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 165, 147, 132, 83, 83, 83, 42, 22, 8, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 165, 165, 132, 132, 83, 42, 42, 22, 22, 22, 22, 8, 8, 2, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 944 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061132 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061132 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061132/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061132 Building REAL250005061133 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061133' /scratch/stefan/7916143/working/building/REAL250005061133 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061133 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061133/0 /scratch/stefan/7916143/working/building/REAL250005061133 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/248 `/scratch/stefan/7916143/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCOC1) `REAL250005061133.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061133 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 37, 78, 119, 119, 119, 201, 201, 201, 201, 37, 37, 37, 37, 14, 14, 4, 1, 78, 78, 119, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061133 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 39, 89, 151, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 9, 1, 1, 1, 1, 1, 92, 92, 92, 92, 150, 151, 201, 201, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 884 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061133 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061133 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061133/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061133 Building REAL250005061134 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061134' /scratch/stefan/7916143/working/building/REAL250005061134 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061134 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061134/0 /scratch/stefan/7916143/working/building/REAL250005061134 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/249 `/scratch/stefan/7916143/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061134.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061134 none CCC(OC)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 189, 123, 189, 190, 123, 123, 59, 29, 12, 29, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 189, 190, 190, 190, 123, 59, 59, 31, 31, 31, 31, 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: 892 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061134 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061134 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061134/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061134 Building REAL250005061135 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061135' /scratch/stefan/7916143/working/building/REAL250005061135 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061135 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061135/0 /scratch/stefan/7916143/working/building/REAL250005061135 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/250 `/scratch/stefan/7916143/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061135.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061135 none COC(C)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 193, 201, 88, 88, 88, 51, 23, 10, 22, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 193, 193, 88, 51, 51, 24, 24, 24, 24, 10, 10, 3, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 867 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061135 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061135 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061135/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061135 Building REAL250005061136 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061136' /scratch/stefan/7916143/working/building/REAL250005061136 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061136 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061136/0 /scratch/stefan/7916143/working/building/REAL250005061136 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/251 `/scratch/stefan/7916143/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061136.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061136 none C=CCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 188, 86, 86, 86, 50, 26, 10, 25, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 188, 188, 86, 50, 50, 26, 26, 26, 26, 10, 10, 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: 869 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061136 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061136 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061136/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061136 Building REAL250005061137 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061137' /scratch/stefan/7916143/working/building/REAL250005061137 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061137 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061137/0 /scratch/stefan/7916143/working/building/REAL250005061137 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/252 `/scratch/stefan/7916143/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061137.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061137 none CCOCCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 197, 116, 116, 116, 99, 54, 23, 55, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 198, 198, 197, 197, 116, 98, 99, 57, 57, 57, 57, 23, 23, 5, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 897 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061137 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061137 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061137/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061137 Building REAL250005061138 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061138' /scratch/stefan/7916143/working/building/REAL250005061138 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061138 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061138/0 /scratch/stefan/7916143/working/building/REAL250005061138 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/253 `/scratch/stefan/7916143/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061138.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061138 none COCC(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 186, 97, 186, 97, 97, 52, 25, 11, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 186, 186, 186, 186, 97, 52, 52, 26, 26, 26, 26, 11, 11, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 887 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061138 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061138 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061138/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061138 Building REAL250005061139 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061139' /scratch/stefan/7916143/working/building/REAL250005061139 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061139 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061139/0 /scratch/stefan/7916143/working/building/REAL250005061139 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/254 `/scratch/stefan/7916143/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061139.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061139 none C=CCOCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 100, 67, 67, 67, 32, 19, 8, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 100, 100, 67, 32, 32, 19, 19, 19, 19, 8, 8, 2, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 840 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061139 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061139 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061139/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061139 Building REAL250005061140 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061140' /scratch/stefan/7916143/working/building/REAL250005061140 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061140 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061140/0 /scratch/stefan/7916143/working/building/REAL250005061140 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/255 `/scratch/stefan/7916143/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=COC=N1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061140.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061140 none CC(CNC(=O)C1=COC=N1)CNC(=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', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 5, 5, 1, 5, 1, 1, 1, 1, 1, 62, 142, 194, 194, 194, 201, 201, 201, 201, 201, 67, 67, 67, 67, 24, 24, 5, 1, 1, 141, 142, 194, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 801 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061140 none CC(CNC(=O)C1=COC=N1)CNC(=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', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 79, 147, 200, 200, 200, 201, 201, 201, 201, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 145, 147, 200, 201, 201, 35, 35, 9, 1] 201 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 834 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061140 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061140 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061140/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061140 Building REAL250005061141 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061141' /scratch/stefan/7916143/working/building/REAL250005061141 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061141 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061141/0 /scratch/stefan/7916143/working/building/REAL250005061141 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/256 `/scratch/stefan/7916143/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C#N) `REAL250005061141.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061141 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 45, 85, 138, 138, 138, 201, 201, 201, 46, 46, 46, 46, 21, 21, 6, 1, 85, 85, 138, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 869 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061141 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061141 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061141/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061141 Building REAL250005061142 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061142' /scratch/stefan/7916143/working/building/REAL250005061142 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061142 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061142/0 /scratch/stefan/7916143/working/building/REAL250005061142 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/257 `/scratch/stefan/7916143/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061142.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061142 none CCCC(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 173, 88, 173, 88, 88, 49, 27, 12, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 173, 173, 173, 173, 88, 49, 49, 28, 28, 28, 28, 12, 12, 4, 1] 201 rigid atoms, others: [42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 922 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061142 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061142 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061142/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061142 Building REAL250005061143 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061143' /scratch/stefan/7916143/working/building/REAL250005061143 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061143 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061143/0 /scratch/stefan/7916143/working/building/REAL250005061143 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/258 `/scratch/stefan/7916143/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCC1CC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061143.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061143 none CC(CNC(=O)CCC1CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 111, 36, 36, 7, 36, 3, 1, 1, 1, 1, 145, 196, 201, 201, 201, 201, 201, 201, 201, 201, 145, 145, 145, 145, 111, 111, 36, 7, 7, 3, 3, 1, 1, 1, 1, 1, 196, 196, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40]) total number of confs: 920 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061143 none CC(CNC(=O)CCC1CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 18, 34, 58, 58, 58, 146, 157, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 34, 34, 58, 146, 146, 159, 159, 201, 201, 201, 201, 201, 11, 11, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 839 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061143 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061143 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061143/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061143 Building REAL250005061144 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061144' /scratch/stefan/7916143/working/building/REAL250005061144 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061144 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061144/0 /scratch/stefan/7916143/working/building/REAL250005061144 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/259 `/scratch/stefan/7916143/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC=CC1) `REAL250005061144.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061144 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 33, 72, 113, 113, 113, 201, 201, 201, 201, 34, 34, 34, 34, 13, 13, 4, 1, 72, 72, 113, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 720 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061144 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 94, 157, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 9, 1, 1, 1, 1, 1, 95, 95, 95, 95, 157, 157, 201, 201, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 889 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061144 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061144 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061144/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061144 Building REAL250005061145 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061145' /scratch/stefan/7916143/working/building/REAL250005061145 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061145 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061145/0 /scratch/stefan/7916143/working/building/REAL250005061145 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/260 `/scratch/stefan/7916143/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1CCC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061145.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061145 none CC(CNC(=O)CC1CCC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 92, 27, 27, 6, 27, 1, 1, 1, 1, 1, 129, 173, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 129, 129, 92, 92, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 173, 173, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40]) total number of confs: 876 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061145 none CC(CNC(=O)CC1CCC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 35, 63, 94, 94, 94, 158, 201, 201, 201, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 63, 63, 94, 158, 158, 201, 201, 201, 201, 201, 201, 201, 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: 888 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061145 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061145 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061145/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061145 Building REAL250005061146 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061146' /scratch/stefan/7916143/working/building/REAL250005061146 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061146 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061146/0 /scratch/stefan/7916143/working/building/REAL250005061146 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/261 `/scratch/stefan/7916143/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C1CC1) `REAL250005061146.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061146 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 33, 69, 113, 113, 113, 201, 201, 201, 201, 33, 33, 33, 33, 13, 13, 4, 1, 69, 69, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 850 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061146 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 106, 164, 201, 201, 201, 201, 201, 201, 201, 201, 15, 15, 3, 15, 1, 3, 1, 1, 1, 108, 108, 108, 108, 164, 163, 201, 201, 61, 61, 15, 3, 3, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 890 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061146 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061146 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061146/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061146 Building REAL250005061147 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061147' /scratch/stefan/7916143/working/building/REAL250005061147 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061147 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061147/0 /scratch/stefan/7916143/working/building/REAL250005061147 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/262 `/scratch/stefan/7916143/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061147.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061147 none CC=C(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 133, 201, 133, 133, 88, 38, 15, 36, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 133, 88, 88, 39, 39, 39, 39, 15, 15, 4, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061147 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061147 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061147/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061147 Building REAL250005061148 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061148' /scratch/stefan/7916143/working/building/REAL250005061148 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061148 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061148/0 /scratch/stefan/7916143/working/building/REAL250005061148 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/263 `/scratch/stefan/7916143/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(C)C1) `REAL250005061148.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061148 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 33, 73, 107, 107, 107, 201, 201, 201, 201, 33, 33, 33, 33, 13, 13, 4, 1, 73, 73, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 736 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061148 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 85, 150, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 9, 1, 1, 1, 1, 1, 86, 86, 86, 86, 150, 150, 201, 201, 40, 40, 9, 1, 1, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 39, 40, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 869 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061148 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061148 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061148/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061148 Building REAL250005061149 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061149' /scratch/stefan/7916143/working/building/REAL250005061149 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061149 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061149/0 /scratch/stefan/7916143/working/building/REAL250005061149 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/264 `/scratch/stefan/7916143/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=C1CCC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061149.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061149 none CC(CNC(=O)C=C1CCC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 43, 8, 8, 1, 8, 1, 1, 1, 1, 1, 93, 153, 201, 201, 201, 201, 201, 201, 201, 201, 96, 96, 96, 96, 43, 43, 8, 1, 1, 1, 1, 1, 1, 1, 153, 153, 201, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 900 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061149 none CC(CNC(=O)C=C1CCC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 13, 34, 82, 142, 142, 142, 201, 201, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 82, 82, 142, 201, 201, 201, 201, 201, 201, 201, 13, 13, 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: 742 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061149 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061149 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061149/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061149 Building REAL250005061150 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061150' /scratch/stefan/7916143/working/building/REAL250005061150 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061150 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061150/0 /scratch/stefan/7916143/working/building/REAL250005061150 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/265 `/scratch/stefan/7916143/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061150.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061150 none CC(C)=C(F)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 5, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 156, 201, 156, 156, 92, 44, 19, 43, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 156, 92, 92, 46, 46, 46, 46, 19, 19, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 775 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061150 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061150 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061150/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061150 Building REAL250005061151 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061151' /scratch/stefan/7916143/working/building/REAL250005061151 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061151 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061151/0 /scratch/stefan/7916143/working/building/REAL250005061151 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/266 `/scratch/stefan/7916143/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCCC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061151.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061151 none CC(CNC(=O)C1=CCCC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 38, 7, 7, 1, 7, 1, 1, 1, 1, 1, 90, 152, 198, 198, 198, 201, 201, 201, 201, 201, 92, 92, 92, 92, 38, 38, 7, 1, 1, 1, 1, 1, 1, 1, 152, 151, 198, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 857 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061151 none CC(CNC(=O)C1=CCCC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 33, 67, 142, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 141, 142, 201, 201, 201, 201, 201, 201, 201, 201, 33, 33, 9, 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: 816 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061151 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061151 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061151/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061151 Building REAL250005061152 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061152' /scratch/stefan/7916143/working/building/REAL250005061152 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061152 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061152/0 /scratch/stefan/7916143/working/building/REAL250005061152 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/267 `/scratch/stefan/7916143/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1(C)C) `REAL250005061152.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061152 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 43, 97, 155, 155, 155, 201, 201, 201, 201, 44, 44, 44, 44, 16, 16, 4, 1, 97, 97, 155, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 796 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061152 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 82, 149, 201, 201, 201, 201, 201, 201, 201, 201, 8, 8, 1, 8, 1, 1, 1, 1, 1, 87, 87, 87, 87, 149, 149, 201, 201, 36, 36, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 878 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061152 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061152 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061152/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061152 Building REAL250005061153 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061153' /scratch/stefan/7916143/working/building/REAL250005061153 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061153 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061153/0 /scratch/stefan/7916143/working/building/REAL250005061153 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/268 `/scratch/stefan/7916143/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CC1(C)C) `REAL250005061153.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061153 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 41, 97, 154, 154, 154, 201, 201, 201, 201, 201, 42, 42, 42, 42, 14, 14, 3, 1, 97, 97, 154, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 793 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061153 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 83, 146, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 146, 146, 201, 201, 36, 36, 9, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [33, 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, 35, 36, 37, 38, 39, 40]) total number of confs: 863 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061153 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061153 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061153/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061153 Building REAL250005061154 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061154' /scratch/stefan/7916143/working/building/REAL250005061154 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061154 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061154/0 /scratch/stefan/7916143/working/building/REAL250005061154 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/269 `/scratch/stefan/7916143/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1CCCO1) `REAL250005061154.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061154 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [22, 13, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 22, 33, 50, 50, 50, 85, 85, 85, 85, 85, 22, 22, 22, 22, 12, 12, 3, 1, 33, 33, 50, 85, 85, 85, 85, 85, 85] 85 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 313 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061154 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [62, 48, 61, 77, 85, 85, 85, 85, 85, 85, 85, 85, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 77, 76, 85, 85, 48, 48, 13, 1, 1, 1, 1, 1, 1] 85 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 365 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061154 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061154 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061154/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061154 Building REAL250005061155 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061155' /scratch/stefan/7916143/working/building/REAL250005061155 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061155 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061155/0 /scratch/stefan/7916143/working/building/REAL250005061155 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/270 `/scratch/stefan/7916143/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061155.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061155 none CCC(C)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 185, 199, 64, 64, 64, 38, 23, 9, 23, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 199, 199, 199, 199, 185, 185, 64, 38, 38, 23, 23, 23, 23, 9, 9, 3, 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: 834 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061155 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061155 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061155/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061155 Building REAL250005061156 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061156' /scratch/stefan/7916143/working/building/REAL250005061156 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061156 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061156/0 /scratch/stefan/7916143/working/building/REAL250005061156 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/271 `/scratch/stefan/7916143/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061156.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061156 none C#CCCCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 156, 56, 56, 56, 38, 24, 15, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 194, 196, 178, 178, 156, 156, 56, 38, 38, 26, 26, 26, 26, 15, 15, 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: 971 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061156 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061156 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061156/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061156 Building REAL250005061157 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061157' /scratch/stefan/7916143/working/building/REAL250005061157 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061157 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061157/0 /scratch/stefan/7916143/working/building/REAL250005061157 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/272 `/scratch/stefan/7916143/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC(C)(C)O)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061157.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061157 none CC(CNC(=O)CC(C)(C)O)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 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, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 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: [34, 15, 38, 81, 130, 130, 130, 189, 200, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 81, 81, 130, 189, 189, 201, 201, 201, 201, 201, 201, 603, 15, 15, 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: 1486 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061157 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061157 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061157/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061157 Building REAL250005061158 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061158' /scratch/stefan/7916143/working/building/REAL250005061158 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061158 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061158/0 /scratch/stefan/7916143/working/building/REAL250005061158 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/273 `/scratch/stefan/7916143/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061158.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061158 none CC(C)[C@@H](O)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 201, 128, 183, 183, 128, 128, 70, 34, 13, 31, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 549, 128, 70, 70, 35, 35, 35, 35, 13, 13, 4, 1] 603 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1444 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061158 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061158 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061158/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061158 Building REAL250005061159 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061159' /scratch/stefan/7916143/working/building/REAL250005061159 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061159 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061159/0 /scratch/stefan/7916143/working/building/REAL250005061159 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/274 `/scratch/stefan/7916143/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061159.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061159 none CCC(C)=CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 125, 125, 125, 93, 93, 93, 59, 26, 11, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 125, 125, 125, 125, 93, 59, 59, 26, 26, 26, 26, 11, 11, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 957 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061159 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061159 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061159/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061159 Building REAL250005061160 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061160' /scratch/stefan/7916143/working/building/REAL250005061160 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061160 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061160/0 /scratch/stefan/7916143/working/building/REAL250005061160 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/275 `/scratch/stefan/7916143/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C#CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061160.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061160 none CC(C)C#CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', '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, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 150, 60, 23, 61, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 149, 148, 64, 64, 64, 64, 23, 23, 6, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 807 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061160 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061160 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061160/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061160 Building REAL250005061161 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061161' /scratch/stefan/7916143/working/building/REAL250005061161 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061161 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061161/0 /scratch/stefan/7916143/working/building/REAL250005061161 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/276 `/scratch/stefan/7916143/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C#CC1CC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061161.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061161 none CC(CNC(=O)C#CC1CC1)CNC(=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.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 40, 131, 199, 199, 199, 201, 201, 201, 201, 201, 46, 46, 46, 46, 10, 10, 2, 1, 1, 1, 1, 1, 131, 130, 199, 201] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 790 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061161 none CC(CNC(=O)C#CC1CC1)CNC(=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.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 149, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 149, 149, 201, 201, 201, 201, 201, 201, 27, 27, 6, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 799 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061161 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061161 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061161/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061161 Building REAL250005061162 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061162' /scratch/stefan/7916143/working/building/REAL250005061162 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061162 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061162/0 /scratch/stefan/7916143/working/building/REAL250005061162 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/277 `/scratch/stefan/7916143/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061162.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061162 none CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 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, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 151, 151, 151, 111, 52, 22, 50, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 151, 111, 110, 54, 54, 54, 54, 22, 22, 5, 1] 201 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 917 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061162 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061162 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061162/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061162 Building REAL250005061163 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061163' /scratch/stefan/7916143/working/building/REAL250005061163 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061163 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061163/0 /scratch/stefan/7916143/working/building/REAL250005061163 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/278 `/scratch/stefan/7916143/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061163.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061163 none COCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 191, 90, 90, 90, 50, 24, 9, 23, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 191, 90, 50, 50, 25, 25, 25, 25, 9, 9, 3, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 870 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061163 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061163 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061163/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061163 Building REAL250005061164 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061164' /scratch/stefan/7916143/working/building/REAL250005061164 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061164 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061164/0 /scratch/stefan/7916143/working/building/REAL250005061164 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/279 `/scratch/stefan/7916143/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1) `REAL250005061164.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061164 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 38, 78, 102, 102, 102, 201, 201, 38, 38, 38, 38, 15, 15, 4, 1, 78, 78, 102, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 26] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061164 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 41, 86, 148, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 11, 1, 1, 1, 88, 88, 88, 88, 148, 148, 201, 201, 41, 41, 11, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 852 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061164 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061164 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061164/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061164 Building REAL250005061165 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061165' /scratch/stefan/7916143/working/building/REAL250005061165 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061165 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061165/0 /scratch/stefan/7916143/working/building/REAL250005061165 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/280 `/scratch/stefan/7916143/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCC1) `REAL250005061165.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061165 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 38, 75, 101, 101, 101, 201, 201, 201, 38, 38, 38, 38, 16, 16, 4, 1, 75, 75, 101, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 715 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061165 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 81, 152, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 1, 10, 1, 1, 1, 1, 81, 81, 81, 81, 152, 152, 201, 201, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 869 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061165 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061165 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061165/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061165 Building REAL250005061166 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061166' /scratch/stefan/7916143/working/building/REAL250005061166 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061166 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061166/0 /scratch/stefan/7916143/working/building/REAL250005061166 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/281 `/scratch/stefan/7916143/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCCC1) `REAL250005061166.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061166 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 33, 76, 113, 113, 113, 201, 201, 201, 201, 33, 33, 33, 33, 13, 13, 3, 1, 76, 76, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 731 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061166 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 84, 155, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 9, 1, 1, 1, 1, 1, 85, 85, 85, 85, 155, 155, 201, 201, 42, 42, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 885 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061166 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061166 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061166/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061166 Building REAL250005061167 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061167' /scratch/stefan/7916143/working/building/REAL250005061167 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061167 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061167/0 /scratch/stefan/7916143/working/building/REAL250005061167 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/282 `/scratch/stefan/7916143/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061167.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061167 none C=CCCCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 165, 149, 44, 44, 44, 34, 26, 17, 26, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 199, 199, 183, 183, 149, 149, 44, 34, 34, 26, 26, 26, 26, 17, 17, 5, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1004 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061167 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061167 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061167/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061167 Building REAL250005061168 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061168' /scratch/stefan/7916143/working/building/REAL250005061168 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061168 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061168/0 /scratch/stefan/7916143/working/building/REAL250005061168 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/283 `/scratch/stefan/7916143/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061168.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061168 none CCC(C)(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [184, 193, 111, 193, 193, 111, 111, 65, 30, 12, 28, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 193, 193, 193, 193, 193, 111, 65, 65, 30, 30, 30, 30, 12, 12, 4, 1] 201 rigid atoms, others: [42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 998 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061168 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061168 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061168/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061168 Building REAL250005061169 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061169' /scratch/stefan/7916143/working/building/REAL250005061169 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061169 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061169/0 /scratch/stefan/7916143/working/building/REAL250005061169 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/284 `/scratch/stefan/7916143/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(N)=O)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061169.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061169 none CC(CNC(=O)C(N)=O)CNC(=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', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 11, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 6, 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: [64, 25, 66, 127, 193, 193, 193, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 127, 126, 193, 201, 201, 25, 25, 4, 1] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 796 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061169 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061169 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061169/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061169 Building REAL250005061170 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061170' /scratch/stefan/7916143/working/building/REAL250005061170 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061170 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061170/0 /scratch/stefan/7916143/working/building/REAL250005061170 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/285 `/scratch/stefan/7916143/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1CC1C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061170.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061170 none CC(CNC(=O)CC1CC1C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 111, 38, 38, 6, 38, 1, 1, 1, 1, 1, 143, 185, 201, 201, 201, 201, 201, 201, 201, 201, 143, 143, 143, 143, 111, 111, 38, 6, 6, 1, 1, 1, 1, 2, 2, 2, 185, 185, 201, 201] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 883 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061170 none CC(CNC(=O)CC1CC1C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 26, 48, 69, 69, 69, 168, 201, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 48, 48, 69, 168, 168, 201, 201, 201, 201, 201, 201, 201, 15, 15, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 826 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061170 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061170 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061170/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061170 Building REAL250005061171 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061171' /scratch/stefan/7916143/working/building/REAL250005061171 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061171 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061171/0 /scratch/stefan/7916143/working/building/REAL250005061171 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/286 `/scratch/stefan/7916143/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005061171.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061171 none CCC1(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 7, 7, 7, 38, 77, 77, 125, 185, 185, 185, 185, 185, 185, 185, 185, 1, 1, 3, 3, 3, 3, 3, 7, 38, 38, 77, 77, 77, 77, 125, 125, 185, 185, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 37, 38, 39, 40, 19, 20] 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, 35, 36]) total number of confs: 802 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061171 none CCC1(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 185, 82, 82, 82, 56, 28, 11, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 185, 185, 201, 201, 201, 201, 201, 82, 56, 56, 28, 28, 28, 28, 11, 11, 4, 1, 185, 185, 185, 185] 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: 742 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061171 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061171 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061171/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061171 Building REAL250005061172 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061172' /scratch/stefan/7916143/working/building/REAL250005061172 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061172 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061172/0 /scratch/stefan/7916143/working/building/REAL250005061172 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/287 `/scratch/stefan/7916143/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)C) `REAL250005061172.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061172 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 63, 141, 198, 198, 198, 201, 201, 201, 68, 68, 68, 68, 25, 25, 7, 1, 139, 140, 198, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 817 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061172 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061172 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061172/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061172 Building REAL250005061173 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061173' /scratch/stefan/7916143/working/building/REAL250005061173 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061173 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061173/0 /scratch/stefan/7916143/working/building/REAL250005061173 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/288 `/scratch/stefan/7916143/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061173.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061173 none C=C(C)CCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 190, 87, 87, 87, 50, 25, 10, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 190, 190, 87, 50, 50, 25, 25, 25, 25, 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: 880 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061173 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061173 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061173/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061173 Building REAL250005061174 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061174' /scratch/stefan/7916143/working/building/REAL250005061174 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061174 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061174/0 /scratch/stefan/7916143/working/building/REAL250005061174 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/289 `/scratch/stefan/7916143/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(CF)CC1) `REAL250005061174.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061174 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(CF)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 27, 67, 104, 104, 104, 193, 201, 193, 193, 27, 27, 27, 27, 11, 11, 4, 1, 67, 67, 104, 201, 201, 193, 193, 193, 193] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 745 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061174 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(CF)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 138, 192, 192, 192, 193, 193, 193, 193, 193, 7, 7, 1, 7, 1, 1, 9, 1, 1, 69, 69, 69, 69, 138, 137, 192, 193, 34, 34, 7, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 848 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061174 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061174 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061174/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061174 Building REAL250005061175 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061175' /scratch/stefan/7916143/working/building/REAL250005061175 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061175 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061175/0 /scratch/stefan/7916143/working/building/REAL250005061175 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/290 `/scratch/stefan/7916143/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C(C)C) `REAL250005061175.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061175 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 76, 132, 132, 132, 198, 198, 201, 201, 36, 36, 36, 36, 13, 13, 4, 1, 76, 76, 132, 198, 198, 198, 198, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 861 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061175 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061175 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061175/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061175 Building REAL250005061176 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061176' /scratch/stefan/7916143/working/building/REAL250005061176 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061176 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061176/0 /scratch/stefan/7916143/working/building/REAL250005061176 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/291 `/scratch/stefan/7916143/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H]1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061176.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061176 none CC[C@@H]1C[C@H]1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 85, 85, 129, 180, 180, 180, 182, 182, 182, 182, 182, 3, 3, 3, 3, 3, 1, 1, 12, 53, 53, 85, 85, 85, 85, 129, 129, 180, 182] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061176 none CC[C@@H]1C[C@H]1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 182, 182, 182, 88, 182, 88, 88, 56, 26, 12, 26, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 182, 182, 88, 56, 56, 26, 26, 26, 26, 11, 11, 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: 752 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061176 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061176 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061176/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061176 Building REAL250005061177 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061177' /scratch/stefan/7916143/working/building/REAL250005061177 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061177 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061177/0 /scratch/stefan/7916143/working/building/REAL250005061177 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/292 `/scratch/stefan/7916143/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC12CC2) `REAL250005061177.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061177 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC12CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 31, 67, 108, 108, 108, 201, 201, 201, 201, 31, 31, 31, 31, 14, 14, 4, 1, 67, 67, 108, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061177 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC12CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 101, 163, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 11, 1, 1, 1, 1, 1, 102, 102, 102, 102, 162, 163, 201, 201, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 888 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061177 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061177 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061177/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061177 Building REAL250005061178 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061178' /scratch/stefan/7916143/working/building/REAL250005061178 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061178 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061178/0 /scratch/stefan/7916143/working/building/REAL250005061178 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/293 `/scratch/stefan/7916143/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CCCO1) `REAL250005061178.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061178 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [16, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 16, 25, 41, 41, 41, 72, 72, 72, 72, 72, 16, 16, 16, 16, 10, 10, 4, 1, 25, 25, 41, 72, 72, 72, 72, 72, 72] 72 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 267 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061178 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [53, 41, 53, 66, 72, 72, 72, 72, 72, 72, 72, 72, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 66, 66, 72, 72, 41, 41, 12, 1, 1, 1, 1, 1, 1] 72 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 307 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061178 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061178 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061178/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061178 Building REAL250005061179 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061179' /scratch/stefan/7916143/working/building/REAL250005061179 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061179 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061179/0 /scratch/stefan/7916143/working/building/REAL250005061179 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/294 `/scratch/stefan/7916143/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1(C)CC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061179.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061179 none CC(CNC(=O)CC1(C)CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 75, 17, 17, 5, 17, 1, 1, 1, 1, 1, 126, 170, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 127, 127, 75, 75, 17, 5, 5, 2, 2, 2, 1, 1, 1, 1, 170, 169, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 898 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061179 none CC(CNC(=O)CC1(C)CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 62, 96, 96, 96, 196, 201, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 62, 61, 96, 196, 196, 201, 201, 201, 201, 201, 201, 201, 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: 858 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061179 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061179 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061179/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061179 Building REAL250005061180 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061180' /scratch/stefan/7916143/working/building/REAL250005061180 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061180 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061180/0 /scratch/stefan/7916143/working/building/REAL250005061180 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/295 `/scratch/stefan/7916143/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CC1) `REAL250005061180.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061180 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 33, 80, 107, 107, 107, 201, 201, 201, 37, 37, 37, 37, 12, 12, 4, 1, 80, 79, 107, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 769 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061180 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 73, 145, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 7, 1, 1, 1, 1, 79, 79, 79, 79, 145, 145, 201, 201, 31, 31, 7, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 851 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061180 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061180 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061180/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061180 Building REAL250005061181 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061181' /scratch/stefan/7916143/working/building/REAL250005061181 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061181 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061181/0 /scratch/stefan/7916143/working/building/REAL250005061181 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/296 `/scratch/stefan/7916143/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CNC=C1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061181.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061181 none CC(CNC(=O)C1=CNC=C1)CNC(=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', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 29, 5, 5, 1, 5, 1, 1, 1, 1, 1, 82, 157, 200, 200, 200, 201, 201, 201, 201, 201, 85, 85, 85, 85, 29, 29, 5, 1, 1, 1, 1, 156, 157, 200, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 865 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061181 none CC(CNC(=O)C1=CNC=C1)CNC(=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', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 38, 90, 130, 130, 129, 201, 201, 201, 201, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 90, 89, 130, 201, 201, 201, 201, 17, 17, 6, 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: 665 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061181 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061181 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061181/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061181 Building REAL250005061182 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061182' /scratch/stefan/7916143/working/building/REAL250005061182 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061182 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061182/0 /scratch/stefan/7916143/working/building/REAL250005061182 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/297 `/scratch/stefan/7916143/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CN=CO1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061182.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061182 none CC(CNC(=O)C1=CN=CO1)CNC(=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', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 70, 143, 198, 198, 198, 201, 201, 201, 201, 201, 72, 72, 72, 72, 30, 30, 7, 1, 1, 143, 143, 198, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 844 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061182 none CC(CNC(=O)C1=CN=CO1)CNC(=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', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 66, 133, 185, 185, 185, 201, 201, 201, 201, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 132, 132, 185, 201, 201, 30, 30, 7, 1] 201 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 802 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061182 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061182 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061182/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061182 Building REAL250005061183 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061183' /scratch/stefan/7916143/working/building/REAL250005061183 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061183 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061183/0 /scratch/stefan/7916143/working/building/REAL250005061183 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/298 `/scratch/stefan/7916143/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061183.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061183 none C=CC(C)(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 119, 201, 201, 119, 119, 70, 32, 11, 30, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 70, 70, 32, 32, 32, 32, 11, 11, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 868 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061183 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061183 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061183/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061183 Building REAL250005061184 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061184' /scratch/stefan/7916143/working/building/REAL250005061184 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061184 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061184/0 /scratch/stefan/7916143/working/building/REAL250005061184 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/299 `/scratch/stefan/7916143/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1C) `REAL250005061184.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061184 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 31, 66, 101, 101, 101, 201, 201, 201, 201, 201, 31, 31, 31, 31, 11, 11, 3, 1, 66, 66, 101, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061184 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 92, 151, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 151, 150, 201, 201, 53, 53, 13, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 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, 35, 36, 37]) total number of confs: 856 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061184 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061184 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061184/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061184 Building REAL250005061185 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061185' /scratch/stefan/7916143/working/building/REAL250005061185 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061185 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061185/0 /scratch/stefan/7916143/working/building/REAL250005061185 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/300 `/scratch/stefan/7916143/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CCC1) `REAL250005061185.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061185 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 34, 71, 105, 105, 105, 201, 201, 201, 201, 35, 35, 35, 35, 15, 15, 4, 1, 71, 71, 105, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 738 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061185 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 71, 144, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 7, 1, 1, 1, 1, 1, 74, 74, 74, 74, 144, 144, 201, 201, 33, 33, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 851 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061185 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061185 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061185/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061185 Building REAL250005061186 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061186' /scratch/stefan/7916143/working/building/REAL250005061186 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061186 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061186/0 /scratch/stefan/7916143/working/building/REAL250005061186 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/301 `/scratch/stefan/7916143/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061186.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061186 none CCC(F)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 174, 139, 174, 139, 139, 70, 34, 12, 32, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 174, 139, 70, 70, 37, 37, 37, 37, 12, 12, 4, 1] 201 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 882 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061186 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061186 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061186/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061186 Building REAL250005061187 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061187' /scratch/stefan/7916143/working/building/REAL250005061187 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061187 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061187/0 /scratch/stefan/7916143/working/building/REAL250005061187 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/302 `/scratch/stefan/7916143/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCCF)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061187.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061187 none CC(CNC(=O)CCCF)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 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, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 25, 43, 77, 77, 77, 179, 198, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 43, 43, 77, 179, 179, 201, 201, 201, 201, 13, 13, 4, 1] 201 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 888 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061187 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061187 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061187/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061187 Building REAL250005061188 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061188' /scratch/stefan/7916143/working/building/REAL250005061188 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061188 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061188/0 /scratch/stefan/7916143/working/building/REAL250005061188 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/303 `/scratch/stefan/7916143/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1C[C@@H]1C) `REAL250005061188.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061188 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 31, 67, 102, 102, 102, 201, 201, 201, 201, 201, 31, 31, 31, 31, 12, 12, 4, 1, 67, 67, 102, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 720 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061188 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 54, 91, 150, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 149, 150, 201, 201, 54, 54, 13, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 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, 35, 36, 37]) total number of confs: 849 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061188 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061188 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061188/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061188 Building REAL250005061189 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061189' /scratch/stefan/7916143/working/building/REAL250005061189 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061189 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061189/0 /scratch/stefan/7916143/working/building/REAL250005061189 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/304 `/scratch/stefan/7916143/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NNN=C1) `REAL250005061189.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061189 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NNN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 4, 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: [15, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 15, 29, 39, 39, 39, 57, 57, 57, 57, 15, 15, 15, 15, 9, 9, 4, 1, 29, 29, 39, 57, 57] 57 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061189 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NNN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 4, 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: [27, 16, 27, 48, 56, 56, 56, 57, 57, 57, 57, 57, 6, 6, 1, 6, 1, 1, 1, 1, 1, 27, 27, 27, 27, 48, 48, 56, 57, 16, 16, 6, 1, 1] 57 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061189 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061189/1 /scratch/stefan/7916143/working/building/REAL250005061189 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/305 `/scratch/stefan/7916143/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CN=NN1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061189.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061189 none CC(CNC(=O)C1=CN=NN1)CNC(=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', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [60, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 60, 108, 147, 147, 147, 147, 147, 147, 147, 147, 62, 62, 62, 62, 29, 29, 7, 1, 1, 108, 108, 147, 147] 147 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 619 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061189 none CC(CNC(=O)C1=CN=NN1)CNC(=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', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [46, 23, 46, 94, 127, 127, 127, 147, 147, 147, 147, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 94, 94, 127, 147, 147, 23, 23, 4, 1] 147 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 560 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061189 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061189 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061189/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061189/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061189 Building REAL250005061190 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061190' /scratch/stefan/7916143/working/building/REAL250005061190 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061190 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061190/0 /scratch/stefan/7916143/working/building/REAL250005061190 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/306 `/scratch/stefan/7916143/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CO)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061190.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061190 none CC(CNC(=O)CO)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 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 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [27, 17, 27, 38, 51, 51, 51, 65, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 38, 38, 51, 65, 65, 195, 17, 17, 7, 1] 195 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: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061190 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061190 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061190/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061190 Building REAL250005061191 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061191' /scratch/stefan/7916143/working/building/REAL250005061191 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061191 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061191/0 /scratch/stefan/7916143/working/building/REAL250005061191 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/307 `/scratch/stefan/7916143/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CC(N)=O)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061191.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061191 none CC(CNC(=O)C=CC(N)=O)CNC(=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', 'C.2', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 12, 14, 14, 14, 20, 20, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 12, 12, 14, 20, 20, 21, 21, 7, 7, 2, 1] 21 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: 89 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061191 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061191 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061191/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061191 Building REAL250005061192 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061192' /scratch/stefan/7916143/working/building/REAL250005061192 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061192 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061192/0 /scratch/stefan/7916143/working/building/REAL250005061192 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/308 `/scratch/stefan/7916143/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061192.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061192 none COC(=O)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 160, 201, 69, 69, 69, 43, 20, 9, 20, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 160, 160, 69, 43, 43, 20, 20, 20, 20, 9, 9, 3, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 807 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061192 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061192 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061192/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061192 Building REAL250005061193 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061193' /scratch/stefan/7916143/working/building/REAL250005061193 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061193 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061193/0 /scratch/stefan/7916143/working/building/REAL250005061193 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/309 `/scratch/stefan/7916143/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061193.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061193 none CSC=CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 182, 113, 113, 113, 65, 29, 11, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 182, 182, 113, 65, 65, 29, 29, 29, 29, 11, 11, 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: 713 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061193 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061193 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061193/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061193 Building REAL250005061194 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061194' /scratch/stefan/7916143/working/building/REAL250005061194 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061194 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061194/0 /scratch/stefan/7916143/working/building/REAL250005061194 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/310 `/scratch/stefan/7916143/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCC(N)=O)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061194.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061194 none CC(CNC(=O)CCC(N)=O)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 11, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 15, 22, 35, 53, 53, 53, 116, 124, 125, 125, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 35, 35, 53, 116, 116, 124, 124, 125, 125, 15, 15, 4, 1] 125 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: 546 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061194 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061194 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061194/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061194 Building REAL250005061195 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061195' /scratch/stefan/7916143/working/building/REAL250005061195 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061195 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061195/0 /scratch/stefan/7916143/working/building/REAL250005061195 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/311 `/scratch/stefan/7916143/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCO1) `REAL250005061195.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061195 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [34, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 34, 51, 76, 76, 76, 112, 112, 112, 35, 35, 35, 35, 19, 19, 5, 1, 51, 51, 76, 112, 112, 112, 112, 112] 112 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 427 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061195 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [71, 47, 70, 102, 112, 112, 112, 112, 112, 112, 112, 112, 11, 11, 1, 11, 1, 1, 1, 1, 71, 71, 71, 71, 101, 102, 112, 112, 47, 47, 11, 1, 1, 1, 1, 1] 112 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 487 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061195 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061195 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061195/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061195 Building REAL250005061196 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061196' /scratch/stefan/7916143/working/building/REAL250005061196 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061196 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061196/0 /scratch/stefan/7916143/working/building/REAL250005061196 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/312 `/scratch/stefan/7916143/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCCO1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061196.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061196 none CC(CNC(=O)C1=CCCO1)CNC(=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', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 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, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 7, 7, 1, 7, 1, 1, 1, 1, 1, 80, 152, 199, 199, 199, 201, 201, 201, 201, 201, 83, 83, 83, 83, 34, 34, 8, 1, 1, 1, 1, 1, 152, 151, 199, 201] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 852 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061196 none CC(CNC(=O)C1=CCCO1)CNC(=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', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 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, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 64, 128, 184, 184, 184, 201, 201, 201, 201, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 127, 128, 184, 201, 201, 201, 201, 201, 29, 29, 8, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 768 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061196 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061196 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061196/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061196 Building REAL250005061197 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061197' /scratch/stefan/7916143/working/building/REAL250005061197 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061197 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061197/0 /scratch/stefan/7916143/working/building/REAL250005061197 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/313 `/scratch/stefan/7916143/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1COC1) `REAL250005061197.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061197 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 44, 88, 136, 136, 136, 201, 201, 201, 45, 45, 45, 45, 18, 18, 4, 1, 87, 88, 136, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 757 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061197 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 49, 97, 163, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 1, 10, 1, 1, 1, 1, 100, 100, 100, 100, 161, 163, 201, 201, 49, 49, 10, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 881 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061197 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061197 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061197/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061197 Building REAL250005061198 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061198' /scratch/stefan/7916143/working/building/REAL250005061198 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061198 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061198/0 /scratch/stefan/7916143/working/building/REAL250005061198 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/314 `/scratch/stefan/7916143/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CCO)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061198.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061198 none CC(CNC(=O)C=CCO)CNC(=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', 'C.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 4, 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: [24, 9, 26, 65, 118, 118, 118, 194, 194, 201, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 65, 65, 118, 194, 194, 201, 201, 603, 9, 9, 3, 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: 1363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061198 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061198 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061198/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061198 Building REAL250005061199 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061199' /scratch/stefan/7916143/working/building/REAL250005061199 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061199 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061199/0 /scratch/stefan/7916143/working/building/REAL250005061199 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/315 `/scratch/stefan/7916143/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061199.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061199 none CC=CC(O)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 12, 1, 11, 8, 5, 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, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 189, 127, 189, 127, 127, 66, 31, 11, 30, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 189, 567, 127, 66, 66, 34, 34, 34, 34, 11, 11, 3, 1] 603 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 1428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061199 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061199 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061199/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061199 Building REAL250005061200 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061200' /scratch/stefan/7916143/working/building/REAL250005061200 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061200 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061200/0 /scratch/stefan/7916143/working/building/REAL250005061200 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/316 `/scratch/stefan/7916143/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)[NH+](C)C) `REAL250005061200.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061200 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 5 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061200 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061200/1 /scratch/stefan/7916143/working/building/REAL250005061200 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/317 `/scratch/stefan/7916143/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)N(C)C) `REAL250005061200.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061200/1/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: REAL250005061200 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 27, 42, 63, 63, 63, 99, 99, 99, 102, 102, 28, 28, 28, 28, 17, 17, 6, 1, 42, 42, 63, 99, 99, 99, 102, 102, 102, 102, 102, 102] 102 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 440 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061200 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061200 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061200/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061200/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061200 Building REAL250005061201 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061201' /scratch/stefan/7916143/working/building/REAL250005061201 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061201 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061201/0 /scratch/stefan/7916143/working/building/REAL250005061201 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/318 `/scratch/stefan/7916143/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(F)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061201.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061201 none CCC=C(F)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 141, 141, 120, 141, 120, 120, 76, 36, 12, 36, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 141, 120, 76, 76, 39, 39, 39, 39, 12, 12, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 907 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061201 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061201 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061201/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061201 Building REAL250005061202 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061202' /scratch/stefan/7916143/working/building/REAL250005061202 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061202 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061202/0 /scratch/stefan/7916143/working/building/REAL250005061202 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/319 `/scratch/stefan/7916143/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061202.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061202 none CCC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 139, 139, 92, 92, 92, 57, 24, 10, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 139, 139, 92, 57, 57, 24, 24, 24, 24, 10, 10, 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: 916 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061202 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061202 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061202/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061202 Building REAL250005061203 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061203' /scratch/stefan/7916143/working/building/REAL250005061203 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061203 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061203/0 /scratch/stefan/7916143/working/building/REAL250005061203 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/320 `/scratch/stefan/7916143/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCN=[N+]=[N-])CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061203.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061203 none CC(CNC(=O)CCN=[N+]=[N-])CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 8, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 39, 62, 62, 62, 153, 174, 201, 201, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 39, 39, 62, 153, 153, 174, 174, 8, 8, 3, 1] 201 rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 794 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061203 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061203 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061203/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061203 Building REAL250005061204 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061204' /scratch/stefan/7916143/working/building/REAL250005061204 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061204 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061204/0 /scratch/stefan/7916143/working/building/REAL250005061204 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/321 `/scratch/stefan/7916143/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061204.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061204 none C#CCOCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 142, 87, 87, 87, 60, 28, 10, 24, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 142, 142, 87, 60, 60, 28, 28, 28, 28, 10, 10, 3, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 998 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061204 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061204 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061204/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061204 Building REAL250005061205 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061205' /scratch/stefan/7916143/working/building/REAL250005061205 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061205 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061205/0 /scratch/stefan/7916143/working/building/REAL250005061205 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/322 `/scratch/stefan/7916143/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061205.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061205 none CC(O)CCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 194, 201, 177, 98, 98, 98, 52, 27, 10, 27, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 196, 196, 177, 177, 98, 52, 52, 29, 29, 29, 29, 10, 10, 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: 1490 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061205 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061205 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061205/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061205 Building REAL250005061206 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061206' /scratch/stefan/7916143/working/building/REAL250005061206 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061206 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061206/0 /scratch/stefan/7916143/working/building/REAL250005061206 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/323 `/scratch/stefan/7916143/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061206.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061206 none C#CCCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 193, 101, 101, 101, 58, 28, 10, 27, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 193, 193, 101, 58, 58, 29, 29, 29, 29, 10, 10, 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: 870 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061206 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061206 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061206/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061206 Building REAL250005061207 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061207' /scratch/stefan/7916143/working/building/REAL250005061207 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061207 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061207/0 /scratch/stefan/7916143/working/building/REAL250005061207 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/324 `/scratch/stefan/7916143/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061207.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061207 none CC=CC=CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 200, 157, 157, 157, 114, 46, 18, 46, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 157, 113, 114, 50, 50, 50, 50, 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: 802 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061207 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061207 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061207/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061207 Building REAL250005061208 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061208' /scratch/stefan/7916143/working/building/REAL250005061208 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061208 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061208/0 /scratch/stefan/7916143/working/building/REAL250005061208 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/325 `/scratch/stefan/7916143/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061208.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061208 none COCC=CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 132, 99, 99, 59, 59, 59, 48, 37, 22, 38, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 135, 135, 135, 132, 132, 99, 99, 59, 48, 48, 38, 38, 38, 38, 22, 22, 6, 1] 135 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: 589 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061208 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061208 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061208/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061208 Building REAL250005061209 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061209' /scratch/stefan/7916143/working/building/REAL250005061209 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061209 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061209/0 /scratch/stefan/7916143/working/building/REAL250005061209 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/326 `/scratch/stefan/7916143/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061209.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061209 none CCC(C)(O)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [199, 186, 114, 186, 186, 114, 114, 63, 31, 13, 29, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 186, 186, 186, 558, 114, 63, 63, 32, 32, 32, 32, 13, 13, 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: 1466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061209 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061209 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061209/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061209 Building REAL250005061210 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061210' /scratch/stefan/7916143/working/building/REAL250005061210 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061210 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061210/0 /scratch/stefan/7916143/working/building/REAL250005061210 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/327 `/scratch/stefan/7916143/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061210.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061210 none C#CCC(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 96, 170, 96, 96, 50, 24, 10, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 170, 170, 170, 170, 96, 50, 50, 25, 25, 25, 25, 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: 921 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061210 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061210 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061210/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061210 Building REAL250005061211 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061211' /scratch/stefan/7916143/working/building/REAL250005061211 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061211 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061211/0 /scratch/stefan/7916143/working/building/REAL250005061211 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/328 `/scratch/stefan/7916143/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061211.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061211 none C=CC(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 134, 201, 134, 134, 73, 35, 14, 35, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 134, 73, 73, 38, 38, 38, 38, 14, 14, 4, 1] 603 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061211 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061211 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061211/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061211 Building REAL250005061212 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061212' /scratch/stefan/7916143/working/building/REAL250005061212 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061212 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061212/0 /scratch/stefan/7916143/working/building/REAL250005061212 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/329 `/scratch/stefan/7916143/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C12CC1CC2) `REAL250005061212.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061212 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C12CC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 36, 72, 99, 99, 99, 201, 201, 201, 201, 37, 37, 37, 37, 16, 16, 4, 1, 72, 72, 99, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 569 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061212 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C12CC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 78, 150, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 7, 1, 1, 1, 1, 1, 80, 80, 80, 80, 150, 150, 201, 201, 33, 33, 7, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 855 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061212 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061212 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061212/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061212 Building REAL250005061213 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061213' /scratch/stefan/7916143/working/building/REAL250005061213 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061213 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061213/0 /scratch/stefan/7916143/working/building/REAL250005061213 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/330 `/scratch/stefan/7916143/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@H](C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061213.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061213 none C=C[C@H](C)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 173, 201, 201, 81, 81, 81, 46, 23, 11, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 173, 173, 81, 46, 46, 24, 24, 24, 24, 11, 11, 4, 1] 201 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 902 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061213 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061213 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061213/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061213 Building REAL250005061214 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061214' /scratch/stefan/7916143/working/building/REAL250005061214 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061214 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061214/0 /scratch/stefan/7916143/working/building/REAL250005061214 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/331 `/scratch/stefan/7916143/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CC1CC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061214.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061214 none CC(CNC(=O)C=CC1CC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 90, 37, 37, 9, 36, 9, 1, 1, 1, 1, 124, 176, 201, 201, 201, 201, 201, 201, 201, 201, 124, 124, 124, 124, 90, 90, 37, 9, 9, 1, 1, 1, 1, 1, 176, 176, 201, 201] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 850 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061214 none CC(CNC(=O)C=CC1CC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 24, 57, 98, 98, 98, 153, 153, 201, 201, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 56, 57, 98, 153, 153, 201, 201, 201, 201, 201, 9, 9, 3, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 767 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061214 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061214 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061214/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061214 Building REAL250005061215 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061215' /scratch/stefan/7916143/working/building/REAL250005061215 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061215 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061215/0 /scratch/stefan/7916143/working/building/REAL250005061215 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/332 `/scratch/stefan/7916143/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C#N)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061215.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061215 none CCC(C#N)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 185, 117, 185, 185, 117, 117, 56, 28, 11, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 185, 117, 56, 56, 28, 28, 28, 28, 11, 11, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 894 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061215 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061215 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061215/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061215 Building REAL250005061216 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061216' /scratch/stefan/7916143/working/building/REAL250005061216 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061216 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061216/0 /scratch/stefan/7916143/working/building/REAL250005061216 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/333 `/scratch/stefan/7916143/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1C2CCC21) `REAL250005061216.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061216 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1C2CCC21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 43, 103, 160, 160, 160, 201, 201, 201, 201, 45, 45, 45, 45, 19, 19, 4, 1, 103, 102, 160, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 784 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061216 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1C2CCC21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 77, 147, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 1, 10, 1, 1, 1, 1, 1, 80, 80, 80, 80, 146, 147, 201, 201, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 845 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061216 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061216 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061216/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061216 Building REAL250005061217 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061217' /scratch/stefan/7916143/working/building/REAL250005061217 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061217 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061217/0 /scratch/stefan/7916143/working/building/REAL250005061217 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/334 `/scratch/stefan/7916143/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061217.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061217 none C=C1CCC1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 52, 104, 104, 151, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 10, 52, 52, 105, 105, 105, 105, 151, 151, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 22, 23, 24, 25, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 879 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061217 none C=C1CCC1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 128, 128, 128, 71, 33, 12, 31, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 128, 71, 71, 34, 34, 34, 34, 12, 12, 4, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 736 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061217 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061217 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061217/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061217 Building REAL250005061218 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061218' /scratch/stefan/7916143/working/building/REAL250005061218 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061218 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061218/0 /scratch/stefan/7916143/working/building/REAL250005061218 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/335 `/scratch/stefan/7916143/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1[C@H](C)[C@@H]1C) `REAL250005061218.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061218 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1[C@H](C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 71, 107, 107, 107, 201, 201, 201, 201, 201, 201, 32, 32, 32, 32, 12, 12, 2, 1, 71, 71, 107, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 727 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061218 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1[C@H](C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 52, 91, 157, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 157, 157, 201, 201, 52, 52, 11, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 883 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061218 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061218 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061218/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061218 Building REAL250005061219 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061219' /scratch/stefan/7916143/working/building/REAL250005061219 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005061219 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061219/0 /scratch/stefan/7916143/working/building/REAL250005061219 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/336 `/scratch/stefan/7916143/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061219.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061219 none CC[N@H+](C)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 64, 55, 64, 64, 28, 28, 28, 16, 15, 12, 15, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 64, 64, 64, 55, 55, 28, 16, 16, 15, 15, 15, 15, 12, 12, 7, 1] 67 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: 309 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061219 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061219/1 /scratch/stefan/7916143/working/building/REAL250005061219 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/337 `/scratch/stefan/7916143/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061219.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061219/1/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: REAL250005061219 none CC[N@@H+](C)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 64, 56, 64, 64, 28, 28, 28, 16, 15, 12, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 64, 64, 64, 56, 56, 28, 16, 16, 15, 15, 15, 15, 12, 12, 7, 1] 67 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: 305 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061219 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `2' /scratch/stefan/7916143/working/building/REAL250005061219/2 /scratch/stefan/7916143/working/building/REAL250005061219 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 2 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/338 `/scratch/stefan/7916143/working/3D/338' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061219.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005061219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061219/2/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: REAL250005061219 none CCN(C)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 186, 198, 101, 101, 101, 56, 23, 9, 23, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 198, 198, 198, 186, 186, 101, 56, 56, 24, 24, 24, 24, 9, 9, 3, 1] 201 rigid atoms, others: [41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 882 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061219 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061219 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061219/0.* 2: /scratch/stefan/7916143/working/building/REAL250005061219/2.* 1: /scratch/stefan/7916143/working/building/REAL250005061219/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061219 Building REAL250005061220 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061220' /scratch/stefan/7916143/working/building/REAL250005061220 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061220 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061220/0 /scratch/stefan/7916143/working/building/REAL250005061220 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/339 `/scratch/stefan/7916143/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061220.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061220 none CC(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 252 conformations in input total number of sets (complete confs): 252 using faster count positions algorithm for large data unique positions, atoms: [84, 63, 84, 63, 63, 42, 29, 19, 29, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 252, 63, 42, 42, 29, 29, 29, 29, 19, 19, 6, 1] 252 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: 605 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061220 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061220 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061220/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061220 Building REAL250005061221 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061221' /scratch/stefan/7916143/working/building/REAL250005061221 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061221 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061221/0 /scratch/stefan/7916143/working/building/REAL250005061221 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/340 `/scratch/stefan/7916143/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061221.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061221 none CC(=O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 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, 3, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 187, 187, 117, 53, 20, 51, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 187, 117, 117, 56, 56, 56, 56, 20, 20, 4, 1] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 784 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061221 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061221 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061221/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061221 Building REAL250005061222 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061222' /scratch/stefan/7916143/working/building/REAL250005061222 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061222 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061222/0 /scratch/stefan/7916143/working/building/REAL250005061222 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/341 `/scratch/stefan/7916143/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCCC#N)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061222.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061222 none CC(CNC(=O)CCCC#N)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 5, 5, 5, 1, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 38, 58, 58, 58, 154, 165, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 38, 38, 58, 154, 154, 184, 184, 193, 192, 15, 15, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 996 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061222 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061222 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061222/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061222 Building REAL250005061223 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061223' /scratch/stefan/7916143/working/building/REAL250005061223 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061223 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061223/0 /scratch/stefan/7916143/working/building/REAL250005061223 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/342 `/scratch/stefan/7916143/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C#N)CC1) `REAL250005061223.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061223 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C#N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 46, 96, 152, 152, 152, 201, 201, 201, 201, 48, 48, 48, 48, 20, 20, 4, 1, 96, 96, 152, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 777 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061223 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C#N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 77, 150, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 6, 1, 1, 1, 1, 1, 82, 82, 82, 82, 149, 150, 201, 201, 32, 32, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 857 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061223 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061223 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061223/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061223 Building REAL250005061224 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061224' /scratch/stefan/7916143/working/building/REAL250005061224 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061224 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061224/0 /scratch/stefan/7916143/working/building/REAL250005061224 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/343 `/scratch/stefan/7916143/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061224.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061224 none C=C1CC(C(=O)NCC(C)CNC(=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', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 9, 47, 77, 80, 140, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 9, 47, 47, 80, 80, 80, 80, 140, 140, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 20, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 868 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061224 none C=C1CC(C(=O)NCC(C)CNC(=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', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 125, 125, 84, 46, 21, 41, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 125, 84, 84, 46, 46, 46, 46, 21, 21, 4, 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: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061224 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061224 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061224/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061224 Building REAL250005061225 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061225' /scratch/stefan/7916143/working/building/REAL250005061225 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061225 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061225/0 /scratch/stefan/7916143/working/building/REAL250005061225 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/344 `/scratch/stefan/7916143/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(F)CC1) `REAL250005061225.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061225 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 80, 137, 137, 137, 201, 201, 201, 40, 40, 40, 40, 18, 18, 4, 1, 80, 80, 137, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061225 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 58, 112, 164, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 11, 1, 1, 1, 1, 118, 118, 118, 118, 164, 163, 201, 201, 58, 58, 11, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 896 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061225 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061225 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061225/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061225 Building REAL250005061226 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061226' /scratch/stefan/7916143/working/building/REAL250005061226 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061226 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061226/0 /scratch/stefan/7916143/working/building/REAL250005061226 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/345 `/scratch/stefan/7916143/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061226.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061226 none COC(C)(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 136, 200, 200, 136, 136, 72, 37, 16, 37, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 200, 200, 200, 200, 200, 136, 72, 72, 39, 39, 39, 39, 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: 843 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061226 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061226 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061226/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061226 Building REAL250005061227 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061227' /scratch/stefan/7916143/working/building/REAL250005061227 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061227 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061227/0 /scratch/stefan/7916143/working/building/REAL250005061227 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/346 `/scratch/stefan/7916143/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)CC#N) `REAL250005061227.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061227 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)CC#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 31, 57, 90, 90, 90, 169, 169, 201, 201, 31, 31, 31, 31, 16, 16, 4, 1, 57, 57, 90, 169, 169, 169, 169, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 905 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061227 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061227 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061227/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061227 Building REAL250005061228 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061228' /scratch/stefan/7916143/working/building/REAL250005061228 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061228 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061228/0 /scratch/stefan/7916143/working/building/REAL250005061228 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/347 `/scratch/stefan/7916143/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061228.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061228 none CCC1CC1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 12, 12, 12, 55, 89, 90, 132, 180, 180, 180, 184, 184, 184, 184, 184, 3, 3, 3, 3, 3, 1, 1, 1, 1, 12, 55, 55, 90, 90, 90, 90, 132, 132, 180, 184] 201 rigid atoms, others: [1, 2, 3, 4, 5, 26, 27, 28, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 771 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061228 none CCC1CC1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 184, 184, 184, 86, 86, 86, 52, 24, 12, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 184, 184, 184, 184, 86, 52, 52, 24, 24, 24, 24, 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: 738 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061228 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061228 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061228/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061228 Building REAL250005061229 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061229' /scratch/stefan/7916143/working/building/REAL250005061229 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061229 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061229/0 /scratch/stefan/7916143/working/building/REAL250005061229 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/348 `/scratch/stefan/7916143/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061229.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061229 none C=CC(C)(O)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 1, 11, 8, 5, 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, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 140, 201, 201, 140, 140, 73, 32, 13, 32, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 140, 73, 73, 34, 34, 34, 34, 13, 13, 4, 1] 603 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 1457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061229 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061229 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061229/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061229 Building REAL250005061230 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061230' /scratch/stefan/7916143/working/building/REAL250005061230 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061230 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061230/0 /scratch/stefan/7916143/working/building/REAL250005061230 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/349 `/scratch/stefan/7916143/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061230.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061230 none CCCC=CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 151, 151, 87, 87, 87, 71, 40, 22, 45, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 151, 151, 87, 71, 71, 45, 45, 45, 45, 22, 22, 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: 890 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061230 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061230 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061230/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061230 Building REAL250005061231 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061231' /scratch/stefan/7916143/working/building/REAL250005061231 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061231 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061231/0 /scratch/stefan/7916143/working/building/REAL250005061231 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/350 `/scratch/stefan/7916143/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061231.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061231 none CC=C(F)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 163, 200, 163, 163, 104, 52, 23, 52, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 163, 104, 104, 55, 55, 55, 55, 23, 23, 5, 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: 788 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061231 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061231 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061231/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061231 Building REAL250005061232 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061232' /scratch/stefan/7916143/working/building/REAL250005061232 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061232 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061232/0 /scratch/stefan/7916143/working/building/REAL250005061232 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/351 `/scratch/stefan/7916143/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H](C)[NH+](C)C) `REAL250005061232.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061232 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H](C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 5 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061232 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061232/1 /scratch/stefan/7916143/working/building/REAL250005061232 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/352 `/scratch/stefan/7916143/working/3D/352' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H](C)N(C)C) `REAL250005061232.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061232/1/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: REAL250005061232 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H](C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 28, 42, 63, 63, 63, 97, 97, 97, 102, 102, 29, 29, 29, 29, 18, 18, 7, 1, 42, 42, 63, 97, 97, 97, 102, 102, 102, 102, 102, 102] 102 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 429 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061232 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061232 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061232/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061232/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061232 Building REAL250005061233 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061233' /scratch/stefan/7916143/working/building/REAL250005061233 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061233 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061233/0 /scratch/stefan/7916143/working/building/REAL250005061233 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/353 `/scratch/stefan/7916143/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061233.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061233 none CCOC=CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 124, 124, 105, 105, 105, 83, 53, 23, 52, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 134, 134, 134, 134, 134, 124, 124, 105, 82, 83, 54, 54, 54, 54, 23, 23, 5, 1] 134 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: 519 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061233 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061233 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061233/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061233 Building REAL250005061234 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061234' /scratch/stefan/7916143/working/building/REAL250005061234 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061234 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061234/0 /scratch/stefan/7916143/working/building/REAL250005061234 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/354 `/scratch/stefan/7916143/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)OCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061234.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061234 none CC(=O)OCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 5, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 179, 79, 79, 79, 44, 23, 10, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 179, 179, 79, 44, 44, 23, 23, 23, 23, 10, 10, 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: 773 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061234 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061234 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061234/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061234 Building REAL250005061235 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061235' /scratch/stefan/7916143/working/building/REAL250005061235 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061235 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061235/0 /scratch/stefan/7916143/working/building/REAL250005061235 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/355 `/scratch/stefan/7916143/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061235.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061235 none CC(=O)C=CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 175, 114, 114, 114, 65, 30, 12, 27, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 175, 175, 114, 65, 65, 30, 30, 30, 30, 12, 12, 4, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061235 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061235 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061235/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061235 Building REAL250005061236 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061236' /scratch/stefan/7916143/working/building/REAL250005061236 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061236 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061236/0 /scratch/stefan/7916143/working/building/REAL250005061236 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/356 `/scratch/stefan/7916143/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)COC1CC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061236.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061236 none CC(CNC(=O)COC1CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 156, 85, 85, 21, 85, 6, 1, 1, 1, 1, 171, 192, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 171, 171, 156, 156, 85, 21, 21, 1, 1, 1, 1, 1, 192, 192, 201, 201] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 802 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061236 none CC(CNC(=O)COC1CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 17, 27, 42, 42, 42, 144, 181, 201, 201, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 27, 27, 42, 144, 144, 201, 201, 201, 201, 201, 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: 721 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061236 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061236 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061236/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061236 Building REAL250005061237 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061237' /scratch/stefan/7916143/working/building/REAL250005061237 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061237 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061237/0 /scratch/stefan/7916143/working/building/REAL250005061237 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/357 `/scratch/stefan/7916143/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NC=CN1) `REAL250005061237.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061237 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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: [17, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 25, 26, 26, 26, 27, 27, 27, 27, 17, 17, 17, 17, 14, 14, 6, 1, 25, 25, 26, 27, 27, 27] 27 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061237 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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: [29, 14, 29, 44, 51, 51, 51, 51, 51, 51, 51, 51, 6, 6, 1, 6, 1, 1, 1, 1, 1, 29, 29, 29, 29, 44, 44, 51, 51, 14, 14, 6, 1, 1, 1] 51 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 225 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061237 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061237 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061237/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061237 Building REAL250005061238 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061238' /scratch/stefan/7916143/working/building/REAL250005061238 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061238 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061238/0 /scratch/stefan/7916143/working/building/REAL250005061238 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/358 `/scratch/stefan/7916143/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)CO) `REAL250005061238.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061238 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [13, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 21, 32, 32, 32, 59, 59, 61, 13, 13, 13, 13, 8, 8, 2, 1, 21, 21, 32, 59, 59, 59, 59, 61, 61, 183] 183 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 452 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061238 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061238 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061238/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061238 Building REAL250005061239 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061239' /scratch/stefan/7916143/working/building/REAL250005061239 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061239 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061239/0 /scratch/stefan/7916143/working/building/REAL250005061239 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/359 `/scratch/stefan/7916143/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CON=C1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061239.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061239 none CC(CNC(=O)C1=CON=C1)CNC(=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', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 5, 5, 1, 5, 1, 1, 1, 1, 1, 78, 148, 201, 201, 201, 201, 201, 201, 201, 201, 81, 81, 81, 81, 31, 31, 5, 1, 1, 148, 148, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 866 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061239 none CC(CNC(=O)C1=CON=C1)CNC(=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', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 41, 88, 120, 120, 120, 201, 201, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 88, 87, 120, 201, 201, 17, 17, 4, 1] 201 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 657 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061239 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061239 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061239/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061239 Building REAL250005061240 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061240' /scratch/stefan/7916143/working/building/REAL250005061240 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061240 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061240/0 /scratch/stefan/7916143/working/building/REAL250005061240 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/360 `/scratch/stefan/7916143/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCCCO)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061240.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061240 none CC(CNC(=O)CCCCO)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 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, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 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: [22, 14, 22, 36, 59, 59, 59, 153, 179, 201, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 36, 36, 59, 153, 153, 192, 192, 197, 199, 201, 201, 603, 14, 14, 4, 1] 603 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1554 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061240 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061240 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061240/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061240 Building REAL250005061241 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061241' /scratch/stefan/7916143/working/building/REAL250005061241 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061241 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061241/0 /scratch/stefan/7916143/working/building/REAL250005061241 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/361 `/scratch/stefan/7916143/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(=O)C1CC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061241.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061241 none CC(CNC(=O)C(=O)C1CC1)CNC(=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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [74, 60, 32, 32, 11, 32, 1, 11, 1, 1, 1, 73, 81, 81, 81, 81, 84, 84, 84, 84, 84, 74, 74, 74, 74, 60, 60, 32, 1, 1, 1, 1, 1, 81, 81, 81, 84] 84 rigid atoms, others: [32, 6, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061241 none CC(CNC(=O)C(=O)C1CC1)CNC(=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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 14, 17, 27, 27, 27, 60, 60, 84, 84, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 17, 17, 27, 84, 84, 84, 84, 84, 10, 10, 6, 1] 84 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: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061241 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061241 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061241/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061241 Building REAL250005061242 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061242' /scratch/stefan/7916143/working/building/REAL250005061242 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061242 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061242/0 /scratch/stefan/7916143/working/building/REAL250005061242 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/362 `/scratch/stefan/7916143/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1(O)CC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061242.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061242 none CC(CNC(=O)CC1(O)CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [38, 33, 20, 20, 5, 20, 1, 1, 1, 1, 1, 38, 44, 46, 46, 46, 46, 46, 46, 46, 46, 38, 38, 38, 38, 33, 33, 20, 5, 5, 6, 1, 1, 1, 1, 44, 44, 46, 46] 138 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 189 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061242 none CC(CNC(=O)CC1(O)CC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 14, 21, 28, 28, 28, 45, 46, 46, 46, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 21, 21, 28, 45, 45, 138, 46, 46, 46, 46, 10, 10, 4, 1] 138 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: 337 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061242 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061242 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061242/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061242 Building REAL250005061243 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061243' /scratch/stefan/7916143/working/building/REAL250005061243 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061243 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061243/0 /scratch/stefan/7916143/working/building/REAL250005061243 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/363 `/scratch/stefan/7916143/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCC1F) `REAL250005061243.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061243 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 90, 145, 145, 145, 201, 201, 201, 201, 40, 40, 40, 40, 16, 16, 4, 1, 89, 90, 145, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 772 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061243 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CCC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 56, 100, 158, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 11, 1, 1, 1, 1, 1, 103, 103, 103, 103, 158, 158, 201, 201, 56, 56, 11, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 876 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061243 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061243 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061243/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061243 Building REAL250005061244 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061244' /scratch/stefan/7916143/working/building/REAL250005061244 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061244 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061244/0 /scratch/stefan/7916143/working/building/REAL250005061244 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/364 `/scratch/stefan/7916143/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1CF) `REAL250005061244.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061244 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1CF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 28, 52, 84, 84, 84, 197, 197, 197, 197, 197, 201, 28, 28, 28, 28, 11, 11, 4, 1, 52, 52, 84, 197, 197, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 681 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061244 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1CF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 56, 98, 166, 194, 194, 194, 197, 197, 197, 197, 197, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 10, 102, 102, 102, 102, 166, 164, 194, 197, 56, 56, 13, 1, 1, 10, 10] 201 rigid atoms, others: [34, 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, 36, 37]) total number of confs: 917 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061244 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061244 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061244/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061244 Building REAL250005061245 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061245' /scratch/stefan/7916143/working/building/REAL250005061245 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061245 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061245/0 /scratch/stefan/7916143/working/building/REAL250005061245 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/365 `/scratch/stefan/7916143/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CO)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061245.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061245 none CCC(CO)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 50, 35, 50, 52, 35, 35, 19, 12, 7, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 50, 52, 52, 156, 35, 19, 19, 12, 12, 12, 12, 7, 7, 2, 1] 159 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: 390 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061245 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061245 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061245/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061245 Building REAL250005061246 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061246' /scratch/stefan/7916143/working/building/REAL250005061246 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061246 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061246/0 /scratch/stefan/7916143/working/building/REAL250005061246 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/366 `/scratch/stefan/7916143/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@@H]1C#N) `REAL250005061246.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061246 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@@H]1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 51, 103, 160, 160, 160, 201, 201, 201, 201, 201, 201, 54, 54, 54, 54, 24, 24, 7, 1, 103, 103, 160, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061246 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@@H]1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 80, 152, 200, 200, 200, 201, 201, 201, 201, 201, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 151, 152, 200, 201, 40, 40, 10, 1, 1] 201 rigid atoms, others: [34, 35, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 870 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061246 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061246 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061246/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061246 Building REAL250005061247 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061247' /scratch/stefan/7916143/working/building/REAL250005061247 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061247 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061247/0 /scratch/stefan/7916143/working/building/REAL250005061247 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/367 `/scratch/stefan/7916143/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=COCC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061247.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061247 none CC(CNC(=O)C1=COCC1)CNC(=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', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 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, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 9, 9, 1, 9, 1, 1, 1, 1, 1, 89, 156, 200, 200, 200, 201, 201, 201, 201, 201, 92, 92, 92, 92, 41, 41, 9, 1, 1, 1, 1, 1, 156, 156, 200, 201] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 883 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061247 none CC(CNC(=O)C1=COCC1)CNC(=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', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 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, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 41, 96, 156, 156, 156, 201, 201, 201, 201, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 96, 95, 156, 201, 201, 201, 201, 201, 20, 20, 6, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 697 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061247 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061247 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061247/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061247 Building REAL250005061248 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061248' /scratch/stefan/7916143/working/building/REAL250005061248 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061248 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061248/0 /scratch/stefan/7916143/working/building/REAL250005061248 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/368 `/scratch/stefan/7916143/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)CC1) `REAL250005061248.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061248 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [35, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 38, 87, 141, 141, 141, 201, 201, 201, 39, 39, 39, 39, 18, 18, 4, 1, 87, 87, 141, 603, 201, 201, 201, 201] 603 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061248 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [107, 57, 105, 164, 201, 201, 201, 201, 201, 201, 201, 201, 12, 12, 1, 12, 1, 1, 1, 1, 108, 108, 108, 108, 164, 163, 201, 201, 57, 57, 12, 6, 1, 1, 1, 1] 603 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 902 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061248 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061248 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061248/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061248 Building REAL250005061249 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061249' /scratch/stefan/7916143/working/building/REAL250005061249 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061249 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061249/0 /scratch/stefan/7916143/working/building/REAL250005061249 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/369 `/scratch/stefan/7916143/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061249.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061249 none CC(CNC(=O)C1=CCC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [63, 27, 6, 6, 1, 6, 1, 1, 1, 1, 64, 128, 167, 167, 167, 174, 174, 174, 174, 174, 66, 66, 66, 66, 27, 27, 6, 1, 1, 1, 1, 1, 127, 128, 167, 174] 174 rigid atoms, others: [4, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 710 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061249 none CC(CNC(=O)C1=CCC1)CNC(=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', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [74, 38, 77, 144, 174, 174, 174, 174, 174, 174, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 144, 143, 174, 174, 174, 174, 174, 174, 38, 38, 10, 1] 174 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: 743 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061249 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061249 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061249/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061249 Building REAL250005061250 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061250' /scratch/stefan/7916143/working/building/REAL250005061250 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061250 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061250/0 /scratch/stefan/7916143/working/building/REAL250005061250 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/370 `/scratch/stefan/7916143/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)CF) `REAL250005061250.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061250 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)CF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 69, 109, 109, 109, 199, 199, 201, 35, 35, 35, 35, 13, 13, 4, 1, 69, 69, 109, 199, 199, 199, 199, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 844 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061250 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061250 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061250/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061250 Building REAL250005061251 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061251' /scratch/stefan/7916143/working/building/REAL250005061251 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061251 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061251/0 /scratch/stefan/7916143/working/building/REAL250005061251 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/371 `/scratch/stefan/7916143/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061251.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061251 none CC=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 158, 158, 109, 53, 23, 50, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 158, 109, 109, 55, 55, 55, 55, 23, 23, 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: 834 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061251 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061251 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061251/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061251 Building REAL250005061252 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061252' /scratch/stefan/7916143/working/building/REAL250005061252 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061252 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061252/0 /scratch/stefan/7916143/working/building/REAL250005061252 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/372 `/scratch/stefan/7916143/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CC1F) `REAL250005061252.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061252 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 86, 115, 115, 115, 201, 201, 201, 201, 42, 42, 42, 42, 16, 16, 4, 1, 86, 86, 115, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 746 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061252 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 73, 142, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 6, 1, 1, 1, 1, 1, 76, 76, 76, 76, 142, 141, 201, 201, 31, 31, 6, 2, 2, 2, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 851 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061252 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061252 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061252/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061252 Building REAL250005061253 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061253' /scratch/stefan/7916143/working/building/REAL250005061253 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061253 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061253/0 /scratch/stefan/7916143/working/building/REAL250005061253 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/373 `/scratch/stefan/7916143/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CCF)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061253.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061253 none CC(CNC(=O)C=CCF)CNC(=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', 'C.2', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 30, 69, 119, 119, 118, 191, 191, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 68, 69, 119, 191, 191, 201, 201, 13, 13, 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: 790 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061253 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061253 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061253/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061253 Building REAL250005061254 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061254' /scratch/stefan/7916143/working/building/REAL250005061254 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061254 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061254/0 /scratch/stefan/7916143/working/building/REAL250005061254 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/374 `/scratch/stefan/7916143/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(CO)CC1) `REAL250005061254.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061254 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [27, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 29, 61, 111, 111, 111, 192, 201, 192, 192, 29, 29, 29, 29, 12, 12, 4, 1, 61, 61, 111, 201, 201, 603, 192, 192, 192, 192] 603 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1343 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061254 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [61, 30, 60, 133, 191, 191, 191, 192, 192, 192, 192, 192, 7, 7, 1, 7, 1, 1, 8, 1, 1, 61, 61, 61, 61, 133, 133, 191, 192, 30, 30, 7, 8, 8, 24, 1, 1, 1, 1] 603 rigid atoms, others: [35, 36, 37, 38, 14, 16, 17, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 856 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061254 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061254 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061254/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061254 Building REAL250005061255 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061255' /scratch/stefan/7916143/working/building/REAL250005061255 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061255 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061255/0 /scratch/stefan/7916143/working/building/REAL250005061255 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/375 `/scratch/stefan/7916143/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=NO1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061255.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061255 none CC(CNC(=O)C1=CC=NO1)CNC(=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', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 6, 6, 1, 6, 1, 1, 1, 1, 1, 81, 157, 199, 199, 199, 201, 201, 201, 201, 201, 84, 84, 84, 84, 33, 33, 6, 1, 1, 157, 157, 199, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 869 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061255 none CC(CNC(=O)C1=CC=NO1)CNC(=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', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 50, 107, 171, 171, 171, 201, 201, 201, 201, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 107, 107, 171, 201, 201, 22, 22, 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: 725 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061255 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061255 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061255/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061255 Building REAL250005061256 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061256' /scratch/stefan/7916143/working/building/REAL250005061256 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005061256 as failed and skipping /scratch/stefan/7916143/working /scratch/stefan/7916143 `/scratch/stefan/7916143/working/building/REAL250005061256' -> `/scratch/stefan/7916143/failed/REAL250005061256' Building REAL250005061257 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061257' /scratch/stefan/7916143/working/building/REAL250005061257 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061257 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061257/0 /scratch/stefan/7916143/working/building/REAL250005061257 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/376 `/scratch/stefan/7916143/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)O) `REAL250005061257.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061257 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 264 conformations in input total number of sets (complete confs): 264 using faster count positions algorithm for large data unique positions, atoms: [33, 22, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 33, 41, 60, 60, 60, 88, 88, 88, 33, 33, 33, 33, 22, 22, 8, 1, 41, 41, 60, 88, 88, 88, 264] 264 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 634 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061257 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061257 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061257/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061257 Building REAL250005061258 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061258' /scratch/stefan/7916143/working/building/REAL250005061258 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061258 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061258/0 /scratch/stefan/7916143/working/building/REAL250005061258 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/377 `/scratch/stefan/7916143/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061258.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061258 none CON=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 138, 138, 79, 38, 16, 36, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 138, 79, 79, 41, 41, 41, 41, 16, 16, 4, 1] 201 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 788 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061258 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061258 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061258/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061258 Building REAL250005061259 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061259' /scratch/stefan/7916143/working/building/REAL250005061259 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061259 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061259/0 /scratch/stefan/7916143/working/building/REAL250005061259 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/378 `/scratch/stefan/7916143/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061259.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061259 none CC(C)[C@H](O)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 201, 127, 186, 186, 127, 127, 66, 31, 11, 29, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 558, 127, 66, 66, 32, 32, 32, 32, 11, 11, 4, 1] 603 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1416 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061259 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061259 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061259/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061259 Building REAL250005061260 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061260' /scratch/stefan/7916143/working/building/REAL250005061260 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061260 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061260/0 /scratch/stefan/7916143/working/building/REAL250005061260 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/379 `/scratch/stefan/7916143/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005061260.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061260 none C#CC1(C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 36, 78, 77, 143, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 6, 36, 36, 80, 80, 80, 80, 142, 143, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 36, 35, 33, 34, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 859 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061260 none C#CC1(C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 128, 128, 128, 76, 31, 13, 31, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 128, 76, 76, 32, 32, 32, 32, 13, 13, 4, 1, 201, 201, 201, 201] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 740 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061260 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061260 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061260/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061260 Building REAL250005061261 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061261' /scratch/stefan/7916143/working/building/REAL250005061261 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061261 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061261/0 /scratch/stefan/7916143/working/building/REAL250005061261 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/380 `/scratch/stefan/7916143/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC=CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061261.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061261 none C=CC=CCC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 191, 106, 106, 106, 73, 39, 21, 44, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 191, 106, 73, 73, 44, 44, 44, 44, 21, 21, 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: 913 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061261 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061261 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061261/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061261 Building REAL250005061262 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061262' /scratch/stefan/7916143/working/building/REAL250005061262 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061262 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061262/0 /scratch/stefan/7916143/working/building/REAL250005061262 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/381 `/scratch/stefan/7916143/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#C[C@H]1C[C@H]1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061262.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061262 none C#C[C@H]1C[C@H]1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 39, 84, 84, 147, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 7, 39, 39, 86, 86, 86, 86, 147, 147, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061262 none C#C[C@H]1C[C@H]1C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 145, 201, 145, 145, 88, 37, 16, 34, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 145, 88, 88, 37, 37, 37, 37, 16, 16, 4, 1] 201 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 777 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061262 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061262 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061262/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061262 Building REAL250005061263 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061263' /scratch/stefan/7916143/working/building/REAL250005061263 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061263 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061263/0 /scratch/stefan/7916143/working/building/REAL250005061263 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/382 `/scratch/stefan/7916143/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(CC)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061263.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061263 none CC=C(CC)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 88, 158, 201, 88, 88, 59, 24, 10, 23, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 201, 201, 201, 201, 201, 88, 59, 59, 24, 24, 24, 24, 10, 10, 3, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 841 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061263 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061263 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061263/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061263 Building REAL250005061264 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061264' /scratch/stefan/7916143/working/building/REAL250005061264 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061264 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061264/0 /scratch/stefan/7916143/working/building/REAL250005061264 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/383 `/scratch/stefan/7916143/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(F)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061264.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061264 none COC(F)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 107, 197, 107, 107, 64, 35, 13, 33, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 197, 107, 64, 64, 36, 36, 36, 36, 13, 13, 4, 1] 201 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 859 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061264 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061264 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061264/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061264 Building REAL250005061265 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061265' /scratch/stefan/7916143/working/building/REAL250005061265 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061265 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061265/0 /scratch/stefan/7916143/working/building/REAL250005061265 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/384 `/scratch/stefan/7916143/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1C#N) `REAL250005061265.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061265 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 15, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 38, 78, 120, 120, 120, 201, 201, 201, 201, 201, 201, 39, 39, 39, 39, 14, 14, 3, 1, 78, 78, 120, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061265 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 58, 104, 155, 201, 201, 201, 201, 201, 201, 201, 201, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 155, 155, 201, 201, 58, 58, 12, 1, 1] 201 rigid atoms, others: [34, 35, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 853 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061265 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061265 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061265/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061265 Building REAL250005061266 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061266' /scratch/stefan/7916143/working/building/REAL250005061266 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061266 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061266/0 /scratch/stefan/7916143/working/building/REAL250005061266 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/385 `/scratch/stefan/7916143/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1C[C@@H](O)C1) `REAL250005061266.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061266 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1C[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [30, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 33, 75, 122, 122, 122, 201, 201, 201, 201, 201, 201, 33, 33, 33, 33, 14, 14, 5, 1, 75, 75, 122, 201, 201, 603, 201, 201] 603 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 1341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061266 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1C[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 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: [92, 45, 93, 156, 200, 200, 200, 201, 201, 201, 201, 201, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 156, 156, 200, 201, 45, 45, 10, 1, 1, 3, 1, 1] 603 rigid atoms, others: [34, 35, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 879 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061266 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061266 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061266/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061266 Building REAL250005061267 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061267' /scratch/stefan/7916143/working/building/REAL250005061267 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061267 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061267/0 /scratch/stefan/7916143/working/building/REAL250005061267 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/386 `/scratch/stefan/7916143/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)CO) `REAL250005061267.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061267 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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, 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: [21, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 21, 36, 55, 55, 55, 85, 85, 85, 87, 21, 21, 21, 21, 9, 9, 3, 1, 36, 36, 55, 85, 85, 85, 85, 85, 85, 87, 87, 261] 261 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 644 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061267 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061267 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061267/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061267 Building REAL250005061268 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061268' /scratch/stefan/7916143/working/building/REAL250005061268 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061268 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061268/0 /scratch/stefan/7916143/working/building/REAL250005061268 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/387 `/scratch/stefan/7916143/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061268.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061268 none C=CCC(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 162, 65, 162, 65, 65, 39, 21, 9, 21, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 162, 162, 162, 162, 65, 39, 39, 21, 21, 21, 21, 9, 9, 3, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 894 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061268 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061268 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061268/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061268 Building REAL250005061269 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061269' /scratch/stefan/7916143/working/building/REAL250005061269 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061269 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061269/0 /scratch/stefan/7916143/working/building/REAL250005061269 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/388 `/scratch/stefan/7916143/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1C) `REAL250005061269.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061269 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 31, 66, 101, 101, 101, 201, 201, 201, 201, 201, 31, 31, 31, 31, 11, 11, 3, 1, 66, 66, 101, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061269 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 92, 151, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 151, 150, 201, 201, 53, 53, 13, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 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, 35, 36, 37]) total number of confs: 856 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061269 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061269 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061269/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061269 Building REAL250005061270 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061270' /scratch/stefan/7916143/working/building/REAL250005061270 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061270 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061270/0 /scratch/stefan/7916143/working/building/REAL250005061270 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/389 `/scratch/stefan/7916143/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)O) `REAL250005061270.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061270 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 23, 33, 52, 52, 52, 86, 86, 86, 23, 23, 23, 23, 15, 15, 5, 1, 33, 33, 52, 86, 86, 86, 86, 86, 86, 258] 258 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 615 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061270 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061270 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061270/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061270 Building REAL250005061271 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061271' /scratch/stefan/7916143/working/building/REAL250005061271 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061271 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061271/0 /scratch/stefan/7916143/working/building/REAL250005061271 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/390 `/scratch/stefan/7916143/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NOCC1) `REAL250005061271.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061271 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 11, 13, 13, 13, 21, 21, 21, 21, 7, 7, 7, 7, 5, 5, 3, 1, 11, 11, 13, 21, 21, 21, 21] 21 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061271 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1=NOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 16, 18, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 16, 16, 16, 16, 18, 18, 21, 21, 12, 12, 8, 1, 1, 1, 1] 21 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061271 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061271 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061271/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061271 Building REAL250005061272 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061272' /scratch/stefan/7916143/working/building/REAL250005061272 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061272 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061272/0 /scratch/stefan/7916143/working/building/REAL250005061272 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/391 `/scratch/stefan/7916143/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061272.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061272 none CC(C#N)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 188, 201, 201, 99, 99, 99, 54, 29, 12, 29, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 188, 188, 99, 54, 54, 29, 29, 29, 29, 12, 12, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 855 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061272 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061272 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061272/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061272 Building REAL250005061273 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061273' /scratch/stefan/7916143/working/building/REAL250005061273 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061273 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061273/0 /scratch/stefan/7916143/working/building/REAL250005061273 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/392 `/scratch/stefan/7916143/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)CCO) `REAL250005061273.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061273 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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, 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: [31, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 31, 61, 103, 103, 103, 191, 191, 201, 201, 32, 32, 32, 32, 15, 15, 4, 1, 60, 61, 103, 191, 191, 191, 191, 201, 201, 201, 201, 603] 603 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1475 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061273 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061273 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061273/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061273 Building REAL250005061274 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061274' /scratch/stefan/7916143/working/building/REAL250005061274 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061274 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061274/0 /scratch/stefan/7916143/working/building/REAL250005061274 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/393 `/scratch/stefan/7916143/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](O)CF) `REAL250005061274.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061274 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](O)CF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 12, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 4, 7, 7, 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: [34, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 34, 46, 70, 70, 70, 137, 137, 137, 140, 34, 34, 34, 34, 21, 21, 7, 1, 46, 46, 70, 411, 140, 140] 420 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 1007 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061274 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061274 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061274/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061274 Building REAL250005061275 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061275' /scratch/stefan/7916143/working/building/REAL250005061275 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061275 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061275/0 /scratch/stefan/7916143/working/building/REAL250005061275 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/394 `/scratch/stefan/7916143/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)CCC1) `REAL250005061275.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061275 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 336 conformations in input total number of sets (complete confs): 336 using faster count positions algorithm for large data unique positions, atoms: [24, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 23, 43, 66, 66, 66, 112, 112, 112, 112, 24, 24, 24, 24, 14, 14, 5, 1, 43, 43, 66, 336, 112, 112, 112, 112, 112, 112] 336 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 741 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061275 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 336 conformations in input total number of sets (complete confs): 336 using faster count positions algorithm for large data unique positions, atoms: [73, 44, 73, 99, 112, 112, 112, 112, 112, 112, 112, 112, 12, 12, 1, 12, 1, 1, 1, 1, 1, 73, 73, 73, 73, 99, 99, 112, 112, 44, 44, 12, 6, 1, 1, 1, 1, 1, 1] 336 rigid atoms, others: [33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 503 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061275 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061275 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061275/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061275 Building REAL250005061276 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061276' /scratch/stefan/7916143/working/building/REAL250005061276 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061276 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061276/0 /scratch/stefan/7916143/working/building/REAL250005061276 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/395 `/scratch/stefan/7916143/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(O)C1CC1) `REAL250005061276.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061276 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [12, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 16, 18, 18, 18, 37, 37, 42, 42, 12, 12, 12, 12, 10, 10, 6, 1, 16, 16, 18, 37, 111, 42, 42, 42, 42, 42] 126 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061276 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [36, 28, 36, 39, 40, 40, 40, 42, 42, 42, 42, 42, 19, 19, 6, 19, 1, 6, 1, 1, 1, 36, 36, 36, 36, 39, 39, 40, 42, 28, 28, 19, 6, 18, 1, 1, 1, 1, 1] 126 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: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061276 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061276 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061276/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061276 Building REAL250005061277 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061277' /scratch/stefan/7916143/working/building/REAL250005061277 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061277 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061277/0 /scratch/stefan/7916143/working/building/REAL250005061277 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/396 `/scratch/stefan/7916143/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061277.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061277 none C=C(C)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 108, 108, 61, 27, 11, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 108, 61, 61, 28, 28, 28, 28, 11, 11, 4, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 828 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061277 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061277 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061277/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061277 Building REAL250005061278 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061278' /scratch/stefan/7916143/working/building/REAL250005061278 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061278 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061278/0 /scratch/stefan/7916143/working/building/REAL250005061278 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/397 `/scratch/stefan/7916143/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)C#N) `REAL250005061278.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061278 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)(C)C#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 37, 83, 153, 153, 153, 201, 201, 201, 201, 39, 39, 39, 39, 14, 14, 4, 1, 83, 83, 153, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 843 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061278 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061278 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061278/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061278 Building REAL250005061279 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061279' /scratch/stefan/7916143/working/building/REAL250005061279 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061279 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061279/0 /scratch/stefan/7916143/working/building/REAL250005061279 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/398 `/scratch/stefan/7916143/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061279.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061279 none CC(C)=C(C)C(=O)NCC(C)CNC(=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 160, 201, 160, 160, 97, 50, 20, 48, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 160, 97, 97, 51, 51, 51, 51, 20, 20, 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: 789 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061279 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061279 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061279/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061279 Building REAL250005061280 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061280' /scratch/stefan/7916143/working/building/REAL250005061280 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061280 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061280/0 /scratch/stefan/7916143/working/building/REAL250005061280 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/399 `/scratch/stefan/7916143/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061280.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061280 none CNC(=O)CC(=O)NCC(C)CNC(=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 182, 201, 103, 103, 103, 55, 29, 13, 28, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 182, 182, 103, 55, 55, 29, 29, 29, 29, 13, 13, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 838 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061280 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061280 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061280/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061280 Building REAL250005061281 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061281' /scratch/stefan/7916143/working/building/REAL250005061281 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061281 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061281/0 /scratch/stefan/7916143/working/building/REAL250005061281 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/400 `/scratch/stefan/7916143/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(F)C1) `REAL250005061281.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061281 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 37, 81, 114, 114, 114, 201, 201, 201, 201, 37, 37, 37, 37, 16, 16, 4, 1, 81, 81, 114, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 758 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061281 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 86, 157, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 11, 1, 1, 1, 1, 1, 87, 87, 87, 87, 157, 157, 201, 201, 44, 44, 11, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 861 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061281 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061281 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061281/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061281 Building REAL250005061282 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061282' /scratch/stefan/7916143/working/building/REAL250005061282 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061282 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061282/0 /scratch/stefan/7916143/working/building/REAL250005061282 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/401 `/scratch/stefan/7916143/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061282.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061282 none C=CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 30, 12, 28, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 121, 71, 71, 31, 31, 31, 31, 12, 12, 4, 1] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 876 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061282 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061282 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061282/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061282 Building REAL250005061283 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061283' /scratch/stefan/7916143/working/building/REAL250005061283 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061283 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061283/0 /scratch/stefan/7916143/working/building/REAL250005061283 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/402 `/scratch/stefan/7916143/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C[NH+](C)C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061283.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061283 none CC(CNC(=O)C[NH+](C)C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 8, 1, 11, 5, 9, 6, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 4, 7, 6, 7, 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 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 2 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: 5 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061283 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061283/1 /scratch/stefan/7916143/working/building/REAL250005061283 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/403 `/scratch/stefan/7916143/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN(C)C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061283.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061283/1/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: REAL250005061283 none CC(CNC(=O)CN(C)C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 40, 59, 95, 95, 95, 189, 201, 201, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 59, 59, 95, 189, 189, 201, 201, 201, 201, 201, 201, 23, 23, 7, 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: 840 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061283 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061283 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061283/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061283/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061283 Building REAL250005061284 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061284' /scratch/stefan/7916143/working/building/REAL250005061284 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061284 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061284/0 /scratch/stefan/7916143/working/building/REAL250005061284 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/404 `/scratch/stefan/7916143/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC#N)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061284.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061284 none CC(CNC(=O)CC#N)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 23, 45, 90, 140, 140, 140, 201, 201, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 90, 89, 140, 201, 201, 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: 882 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061284 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061284 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061284/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061284 Building REAL250005061285 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061285' /scratch/stefan/7916143/working/building/REAL250005061285 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061285 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061285/0 /scratch/stefan/7916143/working/building/REAL250005061285 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/405 `/scratch/stefan/7916143/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1F) `REAL250005061285.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061285 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 34, 81, 137, 137, 137, 201, 201, 201, 34, 34, 34, 34, 14, 14, 4, 1, 81, 81, 137, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061285 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 115, 167, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 1, 13, 1, 1, 1, 1, 117, 117, 117, 117, 167, 166, 201, 201, 61, 61, 13, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 896 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061285 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061285 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061285/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061285 Building REAL250005061286 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061286' /scratch/stefan/7916143/working/building/REAL250005061286 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061286 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061286/0 /scratch/stefan/7916143/working/building/REAL250005061286 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/406 `/scratch/stefan/7916143/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)[NH+](C)C) `REAL250005061286.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061286 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 5 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061286 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061286/1 /scratch/stefan/7916143/working/building/REAL250005061286 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/407 `/scratch/stefan/7916143/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)N(C)C) `REAL250005061286.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061286/1/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: REAL250005061286 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H](C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 27, 42, 63, 63, 63, 99, 99, 99, 102, 102, 28, 28, 28, 28, 17, 17, 6, 1, 42, 42, 63, 99, 99, 99, 102, 102, 102, 102, 102, 102] 102 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 440 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061286 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061286 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061286/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061286/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061286 Building REAL250005061287 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061287' /scratch/stefan/7916143/working/building/REAL250005061287 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061287 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061287/0 /scratch/stefan/7916143/working/building/REAL250005061287 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/408 `/scratch/stefan/7916143/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCF)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061287.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061287 none CC(CNC(=O)CCF)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 78, 122, 122, 122, 193, 201, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 78, 78, 122, 193, 193, 201, 201, 15, 15, 4, 1] 201 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 847 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061287 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061287 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061287/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061287 Building REAL250005061288 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061288' /scratch/stefan/7916143/working/building/REAL250005061288 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061288 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061288/0 /scratch/stefan/7916143/working/building/REAL250005061288 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/409 `/scratch/stefan/7916143/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1C=CCC1) `REAL250005061288.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061288 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 34, 71, 105, 105, 105, 201, 201, 201, 201, 34, 34, 34, 34, 14, 14, 4, 1, 71, 71, 105, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 699 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061288 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 87, 153, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 1, 10, 1, 1, 1, 1, 1, 88, 88, 88, 88, 153, 153, 201, 201, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 871 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061288 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061288 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061288/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061288 Building REAL250005061289 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061289' /scratch/stefan/7916143/working/building/REAL250005061289 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061289 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061289/0 /scratch/stefan/7916143/working/building/REAL250005061289 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/410 `/scratch/stefan/7916143/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC(C)(C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061289.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061289 none C#CC(C)(C)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 132, 201, 201, 132, 132, 84, 37, 19, 36, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 132, 84, 84, 39, 39, 39, 39, 19, 19, 4, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 911 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061289 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061289 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061289/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061289 Building REAL250005061290 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061290' /scratch/stefan/7916143/working/building/REAL250005061290 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061290 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061290/0 /scratch/stefan/7916143/working/building/REAL250005061290 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/411 `/scratch/stefan/7916143/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061290.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061290 none CO[C@H](C)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 128, 201, 201, 128, 128, 72, 33, 13, 33, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 128, 72, 72, 35, 35, 35, 35, 13, 13, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 853 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061290 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061290 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061290/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061290 Building REAL250005061291 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061291' /scratch/stefan/7916143/working/building/REAL250005061291 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061291 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061291/0 /scratch/stefan/7916143/working/building/REAL250005061291 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/412 `/scratch/stefan/7916143/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061291.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061291 none CC(=O)CCC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 180, 201, 154, 74, 74, 74, 40, 21, 9, 22, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 180, 180, 154, 154, 74, 40, 40, 22, 22, 22, 22, 9, 9, 3, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 871 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061291 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061291 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061291/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061291 Building REAL250005061292 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061292' /scratch/stefan/7916143/working/building/REAL250005061292 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061292 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061292/0 /scratch/stefan/7916143/working/building/REAL250005061292 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/413 `/scratch/stefan/7916143/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H](C)O) `REAL250005061292.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061292 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 264 conformations in input total number of sets (complete confs): 264 using faster count positions algorithm for large data unique positions, atoms: [34, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 34, 42, 61, 61, 61, 88, 88, 88, 34, 34, 34, 34, 21, 21, 8, 1, 42, 42, 61, 88, 88, 88, 264] 264 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 640 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061292 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061292 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061292/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061292 Building REAL250005061293 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061293' /scratch/stefan/7916143/working/building/REAL250005061293 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061293 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061293/0 /scratch/stefan/7916143/working/building/REAL250005061293 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/414 `/scratch/stefan/7916143/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN1CCC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061293.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061293 none CC(CNC(=O)CN1CCC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 109, 41, 41, 6, 41, 1, 1, 1, 1, 1, 153, 183, 198, 198, 198, 201, 201, 201, 201, 201, 157, 157, 157, 157, 109, 109, 41, 6, 6, 1, 1, 1, 1, 1, 1, 183, 181, 198, 201] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39]) total number of confs: 870 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061293 none CC(CNC(=O)CN1CCC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 33, 58, 99, 99, 99, 179, 201, 201, 201, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 58, 57, 99, 179, 179, 201, 201, 201, 201, 201, 201, 22, 22, 7, 1] 201 rigid atoms, others: [39, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 818 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061293 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061293/1 /scratch/stefan/7916143/working/building/REAL250005061293 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/415 `/scratch/stefan/7916143/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C[NH+]1CCC1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061293.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061293 none CC(CNC(=O)C[NH+]1CCC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 5 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061293 none CC(CNC(=O)C[NH+]1CCC1)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 1] 5 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: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061293 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061293 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061293/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061293/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061293 Building REAL250005061294 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061294' /scratch/stefan/7916143/working/building/REAL250005061294 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061294 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061294/0 /scratch/stefan/7916143/working/building/REAL250005061294 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/416 `/scratch/stefan/7916143/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C(C)O) `REAL250005061294.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061294 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C(C)C(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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, 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: [35, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 38, 80, 123, 123, 123, 186, 186, 200, 201, 38, 38, 38, 38, 15, 15, 4, 1, 80, 80, 123, 186, 186, 186, 186, 201, 201, 201, 201, 603] 603 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1477 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061294 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061294 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061294/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061294 Building REAL250005061295 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061295' /scratch/stefan/7916143/working/building/REAL250005061295 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061295 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061295/0 /scratch/stefan/7916143/working/building/REAL250005061295 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/417 `/scratch/stefan/7916143/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061295.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061295 none C=C1CC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 65, 116, 116, 166, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 13, 65, 65, 116, 116, 116, 116, 166, 166, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 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]) total number of confs: 905 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061295 none C=C1CC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 111, 111, 68, 33, 15, 29, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 111, 68, 68, 33, 33, 33, 33, 15, 15, 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: 714 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061295 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061295 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061295/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061295 Building REAL250005061296 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061296' /scratch/stefan/7916143/working/building/REAL250005061296 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061296 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061296/0 /scratch/stefan/7916143/working/building/REAL250005061296 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/418 `/scratch/stefan/7916143/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)COC1) `REAL250005061296.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061296 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 38, 81, 110, 110, 110, 201, 201, 201, 201, 40, 40, 40, 40, 16, 16, 4, 1, 81, 81, 110, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 727 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061296 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(C)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 32, 75, 161, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 6, 1, 1, 1, 1, 1, 79, 79, 79, 79, 161, 161, 201, 201, 32, 32, 6, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 874 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061296 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061296 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061296/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061296 Building REAL250005061297 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061297' /scratch/stefan/7916143/working/building/REAL250005061297 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061297 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061297/0 /scratch/stefan/7916143/working/building/REAL250005061297 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/419 `/scratch/stefan/7916143/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(=O)N1) `REAL250005061297.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061297 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 6, 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: [41, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 42, 79, 121, 121, 121, 182, 182, 182, 182, 44, 44, 44, 44, 20, 20, 7, 1, 79, 79, 121, 182, 182, 182, 182] 182 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 685 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061297 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 6, 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: [106, 58, 104, 157, 182, 182, 182, 182, 182, 182, 182, 182, 11, 11, 1, 11, 1, 1, 1, 1, 1, 107, 107, 107, 107, 156, 157, 182, 182, 58, 58, 11, 1, 1, 1, 1] 182 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 808 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061297 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061297 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061297/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061297 Building REAL250005061298 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061298' /scratch/stefan/7916143/working/building/REAL250005061298 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061298 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061298/0 /scratch/stefan/7916143/working/building/REAL250005061298 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/420 `/scratch/stefan/7916143/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1CC(=O)N1) `REAL250005061298.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061298 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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: [42, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 43, 80, 124, 124, 124, 201, 201, 201, 201, 201, 44, 44, 44, 44, 21, 21, 7, 1, 80, 80, 124, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 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: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061298 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@@H]1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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, 60, 106, 168, 200, 200, 200, 201, 201, 201, 201, 201, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 168, 167, 200, 201, 60, 60, 11, 1, 1, 1] 201 rigid atoms, others: [33, 34, 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]) total number of confs: 884 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061298 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061298 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061298/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061298 Building REAL250005061299 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061299' /scratch/stefan/7916143/working/building/REAL250005061299 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061299 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061299/0 /scratch/stefan/7916143/working/building/REAL250005061299 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/421 `/scratch/stefan/7916143/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061299.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061299 none CCC[C@H](O)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 157, 105, 157, 157, 105, 105, 53, 25, 10, 25, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 471, 105, 53, 53, 26, 26, 26, 26, 10, 10, 3, 1] 603 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061299 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061299 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061299/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061299 Building REAL250005061300 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061300' /scratch/stefan/7916143/working/building/REAL250005061300 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061300 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061300/0 /scratch/stefan/7916143/working/building/REAL250005061300 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/422 `/scratch/stefan/7916143/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(F)CCC1) `REAL250005061300.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061300 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(F)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [25, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 25, 33, 49, 49, 49, 97, 97, 97, 97, 25, 25, 25, 25, 15, 15, 7, 1, 33, 33, 49, 97, 97, 97, 97, 97, 97] 97 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 337 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061300 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(F)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [68, 48, 68, 90, 95, 95, 95, 97, 97, 97, 97, 97, 13, 13, 1, 13, 1, 1, 1, 1, 1, 68, 68, 68, 68, 90, 90, 95, 97, 48, 48, 13, 1, 1, 1, 1, 1, 1] 97 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 423 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061300 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061300 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061300/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061300 Building REAL250005061301 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061301' /scratch/stefan/7916143/working/building/REAL250005061301 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061301 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061301/0 /scratch/stefan/7916143/working/building/REAL250005061301 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/423 `/scratch/stefan/7916143/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CN=CN1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061301.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061301 none CC(CNC(=O)C1=CN=CN1)CNC(=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', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [69, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 69, 135, 183, 183, 183, 187, 187, 187, 187, 187, 72, 72, 72, 72, 31, 31, 7, 1, 1, 1, 135, 134, 183, 187] 187 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 783 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061301 none CC(CNC(=O)C1=CN=CN1)CNC(=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', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [44, 22, 44, 103, 159, 159, 159, 187, 187, 187, 187, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 101, 103, 159, 187, 187, 187, 22, 22, 8, 1] 187 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: 683 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061301 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061301 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061301/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061301 Building REAL250005061302 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061302' /scratch/stefan/7916143/working/building/REAL250005061302 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061302 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061302/0 /scratch/stefan/7916143/working/building/REAL250005061302 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/424 `/scratch/stefan/7916143/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(=O)C1) `REAL250005061302.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061302 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 40, 81, 126, 126, 126, 201, 201, 201, 201, 40, 40, 40, 40, 17, 17, 4, 1, 81, 81, 126, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 756 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061302 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 47, 99, 161, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 1, 10, 1, 1, 1, 1, 1, 100, 100, 100, 100, 161, 161, 201, 201, 47, 47, 10, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 867 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061302 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061302 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061302/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061302 Building REAL250005061303 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061303' /scratch/stefan/7916143/working/building/REAL250005061303 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061303 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061303/0 /scratch/stefan/7916143/working/building/REAL250005061303 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/425 `/scratch/stefan/7916143/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)COC1) `REAL250005061303.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061303 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 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 312 conformations in input total number of sets (complete confs): 312 using faster count positions algorithm for large data unique positions, atoms: [29, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 28, 47, 71, 71, 71, 104, 104, 104, 104, 29, 29, 29, 29, 18, 18, 7, 1, 47, 47, 71, 312, 104, 104, 104, 104] 312 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 694 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061303 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1(O)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 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 312 conformations in input total number of sets (complete confs): 312 using faster count positions algorithm for large data unique positions, atoms: [73, 44, 72, 91, 103, 103, 103, 104, 104, 104, 104, 104, 12, 12, 1, 12, 1, 1, 1, 1, 1, 73, 73, 73, 73, 90, 91, 103, 104, 44, 44, 12, 6, 1, 1, 1, 1] 312 rigid atoms, others: [33, 34, 35, 36, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 462 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061303 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061303 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061303/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061303 Building REAL250005061304 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061304' /scratch/stefan/7916143/working/building/REAL250005061304 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061304 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061304/0 /scratch/stefan/7916143/working/building/REAL250005061304 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/426 `/scratch/stefan/7916143/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1)=C1CC1) `REAL250005061304.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061304 none CC(C(=O)NCC(C)CNC(=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', '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', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 131, 74, 34, 16, 31, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 131, 74, 74, 34, 34, 34, 34, 16, 16, 4, 1, 201, 201, 201, 201] 201 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 727 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061304 none CC(C(=O)NCC(C)CNC(=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', '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', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 57, 100, 102, 160, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 12, 57, 57, 102, 102, 102, 102, 160, 160, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 18, 19, 20] set([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]) total number of confs: 904 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061304 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061304 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061304/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061304 Building REAL250005061305 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061305' /scratch/stefan/7916143/working/building/REAL250005061305 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061305 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061305/0 /scratch/stefan/7916143/working/building/REAL250005061305 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/427 `/scratch/stefan/7916143/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061305.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061305 none CC1=CC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 68, 117, 118, 168, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 13, 68, 68, 118, 118, 118, 118, 168, 168, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 881 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061305 none CC1=CC1C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 106, 106, 106, 61, 28, 11, 26, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 106, 61, 61, 29, 29, 29, 29, 11, 11, 3, 1] 201 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 727 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061305 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061305 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061305/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061305 Building REAL250005061306 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061306' /scratch/stefan/7916143/working/building/REAL250005061306 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061306 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061306/0 /scratch/stefan/7916143/working/building/REAL250005061306 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/428 `/scratch/stefan/7916143/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(=O)N(C)C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061306.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061306 none CC(CNC(=O)C(=O)N(C)C)CNC(=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, 6, 7, 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 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, 11, 13, 13, 13, 19, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 11, 11, 13, 19, 19, 19, 19, 19, 19, 8, 8, 5, 1] 19 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: 71 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061306 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061306 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061306/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061306 Building REAL250005061307 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061307' /scratch/stefan/7916143/working/building/REAL250005061307 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061307 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061307/0 /scratch/stefan/7916143/working/building/REAL250005061307 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/429 `/scratch/stefan/7916143/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)C(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061307.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061307 none CCCC(O)C(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 154, 97, 154, 97, 97, 52, 27, 10, 26, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 154, 462, 97, 52, 52, 27, 27, 27, 27, 10, 10, 3, 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: 1370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061307 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061307 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061307/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061307 Building REAL250005061308 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061308' /scratch/stefan/7916143/working/building/REAL250005061308 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061308 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061308/0 /scratch/stefan/7916143/working/building/REAL250005061308 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/430 `/scratch/stefan/7916143/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061308.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061308 none CCC(O)CC(=O)NCC(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 177, 200, 89, 89, 89, 48, 22, 9, 21, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 600, 177, 177, 89, 48, 48, 23, 23, 23, 23, 9, 9, 3, 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: 1491 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061308 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061308 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061308/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061308 Building REAL250005061309 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061309' /scratch/stefan/7916143/working/building/REAL250005061309 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061309 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061309/0 /scratch/stefan/7916143/working/building/REAL250005061309 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/431 `/scratch/stefan/7916143/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CC(=O)N1) `REAL250005061309.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061309 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 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: [41, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 42, 80, 124, 124, 124, 185, 185, 185, 185, 185, 44, 44, 44, 44, 19, 19, 6, 1, 80, 80, 124, 185, 185, 185] 185 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 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: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061309 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)[C@H]1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 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: [109, 58, 107, 160, 185, 185, 185, 185, 185, 185, 185, 185, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 160, 159, 185, 185, 58, 58, 11, 1, 1, 1] 185 rigid atoms, others: [33, 34, 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]) total number of confs: 814 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061309 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061309 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061309/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061309 Building REAL250005061310 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061310' /scratch/stefan/7916143/working/building/REAL250005061310 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061310 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061310/0 /scratch/stefan/7916143/working/building/REAL250005061310 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/432 `/scratch/stefan/7916143/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005061310.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061310 none COC1(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 12, 12, 12, 52, 100, 103, 147, 198, 198, 198, 201, 201, 201, 201, 201, 1, 1, 5, 5, 5, 12, 52, 52, 104, 104, 104, 104, 147, 147, 198, 201, 1, 1, 1, 1] 201 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: 888 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061310 none COC1(C(=O)NCC(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 134, 134, 134, 71, 30, 10, 27, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 134, 71, 71, 30, 30, 30, 30, 10, 10, 3, 1, 201, 201, 201, 201] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 757 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061310 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061310 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061310/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061310 Building REAL250005061311 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061311' /scratch/stefan/7916143/working/building/REAL250005061311 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061311 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061311/0 /scratch/stefan/7916143/working/building/REAL250005061311 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/433 `/scratch/stefan/7916143/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CSC1) `REAL250005061311.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061311 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CSC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 43, 91, 146, 146, 146, 201, 201, 201, 45, 45, 45, 45, 18, 18, 4, 1, 91, 90, 146, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 775 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061311 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CSC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 51, 100, 166, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 1, 10, 1, 1, 1, 1, 102, 102, 102, 102, 166, 166, 201, 201, 51, 51, 10, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 876 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061311 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061311 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061311/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061311 Building REAL250005061312 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061312' /scratch/stefan/7916143/working/building/REAL250005061312 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061312 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061312/0 /scratch/stefan/7916143/working/building/REAL250005061312 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/434 `/scratch/stefan/7916143/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061312.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061312 none C=CC(=O)NCC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 196, 196, 133, 61, 26, 62, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 196, 133, 132, 66, 66, 66, 66, 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: 832 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061312 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061312 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061312/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061312 Building REAL250005061313 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061313' /scratch/stefan/7916143/working/building/REAL250005061313 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061313 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061313/0 /scratch/stefan/7916143/working/building/REAL250005061313 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/435 `/scratch/stefan/7916143/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(=O)N1) `REAL250005061313.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061313 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 6, 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: [41, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 42, 79, 121, 121, 121, 182, 182, 182, 182, 44, 44, 44, 44, 20, 20, 7, 1, 79, 79, 121, 182, 182, 182, 182] 182 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 685 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061313 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 6, 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: [106, 58, 104, 157, 182, 182, 182, 182, 182, 182, 182, 182, 11, 11, 1, 11, 1, 1, 1, 1, 1, 107, 107, 107, 107, 156, 157, 182, 182, 58, 58, 11, 1, 1, 1, 1] 182 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 808 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061313 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061313 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061313/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061313 Building REAL250005061314 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061314' /scratch/stefan/7916143/working/building/REAL250005061314 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061314 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061314/0 /scratch/stefan/7916143/working/building/REAL250005061314 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/436 `/scratch/stefan/7916143/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(F)C1) `REAL250005061314.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061314 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 37, 81, 114, 114, 114, 201, 201, 201, 201, 37, 37, 37, 37, 16, 16, 4, 1, 81, 81, 114, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 758 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061314 none CC(CNC(=O)C1=CC(=O)[N-]O1)CNC(=O)C1CC(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 86, 157, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 11, 1, 1, 1, 1, 1, 87, 87, 87, 87, 157, 157, 201, 201, 44, 44, 11, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 861 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061314 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061314 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061314/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061314 Building REAL250005061315 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061315' /scratch/stefan/7916143/working/building/REAL250005061315 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061315 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061315/0 /scratch/stefan/7916143/working/building/REAL250005061315 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/437 `/scratch/stefan/7916143/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=NO1)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061315.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061315 none CC(CNC(=O)C1=CC=NO1)CNC(=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', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 6, 6, 1, 6, 1, 1, 1, 1, 1, 81, 157, 199, 199, 199, 201, 201, 201, 201, 201, 84, 84, 84, 84, 33, 33, 6, 1, 1, 157, 157, 199, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 869 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061315 none CC(CNC(=O)C1=CC=NO1)CNC(=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', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 50, 107, 171, 171, 171, 201, 201, 201, 201, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 107, 107, 171, 201, 201, 22, 22, 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: 725 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061315 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061315 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061315/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061315 Building REAL250005061316 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061316' /scratch/stefan/7916143/working/building/REAL250005061316 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061316 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061316/0 /scratch/stefan/7916143/working/building/REAL250005061316 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/438 `/scratch/stefan/7916143/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005061316.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061316 none CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [113, 43, 43, 43, 10, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 1, 113, 113, 113, 113, 113, 43, 10, 10, 1, 1, 1, 29, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 459 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061316 none CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 154, 154, 154, 99, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 201, 201, 201, 201, 201, 154, 99, 99, 29, 29, 29, 1, 29, 29, 29, 29] 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: 786 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061316 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061316 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061316/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061316 Building REAL250005061317 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061317' /scratch/stefan/7916143/working/building/REAL250005061317 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061317 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061317/0 /scratch/stefan/7916143/working/building/REAL250005061317 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/439 `/scratch/stefan/7916143/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005061317.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061317 none CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 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] dock color type numbers: [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] 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: [50, 50, 50, 10, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 1, 50, 50, 50, 50, 10, 10, 1, 1, 1, 37, 1, 1, 1, 1] 147 rigid atoms, others: [32, 4, 5, 6, 7, 8, 16, 17, 18, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061317 none CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 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] dock color type numbers: [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] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 119, 37, 37, 37, 10, 1, 10, 1, 1, 1, 1, 1, 1, 37, 37, 37, 147, 147, 147, 147, 119, 119, 37, 37, 37, 1, 37, 37, 37, 37] 147 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 500 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061317 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061317 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061317/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061317 Building REAL250005061318 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061318' /scratch/stefan/7916143/working/building/REAL250005061318 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061318 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061318/0 /scratch/stefan/7916143/working/building/REAL250005061318 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/440 `/scratch/stefan/7916143/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1)C1CC1) `REAL250005061318.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061318 none O=C(NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 9, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 1, 36, 103, 103, 36, 9, 9, 1, 1, 1, 19, 1, 1, 1, 1, 103, 103, 103, 103, 103] 201 rigid atoms, others: [3, 4, 5, 6, 7, 15, 16, 17, 24, 25, 26, 28, 29, 30, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 27, 32, 33, 34, 35, 36]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061318 none O=C(NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 81, 19, 19, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 128, 201, 201, 128, 81, 81, 19, 19, 19, 1, 19, 19, 19, 19, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 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: 683 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005061318 none O=C(NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 51, 102, 102, 102, 184, 184, 201, 201, 201, 201, 201, 102, 102, 102, 1, 1, 1, 11, 51, 51, 102, 102, 102, 201, 102, 102, 102, 102, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 33, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 609 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061318 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061318 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061318/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061318 Building REAL250005061319 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061319' /scratch/stefan/7916143/working/building/REAL250005061319 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061319 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061319/0 /scratch/stefan/7916143/working/building/REAL250005061319 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/441 `/scratch/stefan/7916143/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005061319.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061319 none COCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [108, 89, 35, 35, 35, 9, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 1, 108, 108, 108, 90, 90, 35, 9, 9, 1, 1, 1, 21, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061319 none COCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 141, 141, 141, 77, 21, 21, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 201, 201, 201, 201, 201, 141, 77, 77, 21, 21, 21, 1, 21, 21, 21, 21] 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: 775 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061319 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061319 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061319/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061319 Building REAL250005061320 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061320' /scratch/stefan/7916143/working/building/REAL250005061320 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061320 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061320/0 /scratch/stefan/7916143/working/building/REAL250005061320 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/442 `/scratch/stefan/7916143/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005061320.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061320 none CCCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 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'] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 97, 30, 30, 30, 8, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 1, 1, 105, 105, 105, 105, 105, 97, 97, 30, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 35, 36, 37, 6, 7, 8, 9, 10, 18, 19, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 478 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061320 none CCCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 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'] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 111, 111, 111, 62, 15, 15, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 201, 201, 201, 201, 201, 199, 199, 111, 62, 62, 15, 15, 15, 1, 15, 15, 15, 15] 201 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 811 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061320 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061320 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061320/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061320 Building REAL250005061321 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061321' /scratch/stefan/7916143/working/building/REAL250005061321 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061321 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061321/0 /scratch/stefan/7916143/working/building/REAL250005061321 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/443 `/scratch/stefan/7916143/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005061321.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061321 none CC(C)C(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 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'] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 38, 105, 38, 38, 8, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 1, 105, 105, 105, 105, 105, 105, 105, 38, 8, 8, 1, 1, 1, 22, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 35, 36, 37, 6, 7, 8, 9, 10, 18, 19, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 422 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061321 none CC(C)C(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 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'] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 173, 201, 173, 173, 97, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 201, 201, 201, 201, 201, 201, 201, 173, 97, 97, 22, 22, 22, 1, 22, 22, 22, 22] 201 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 733 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061321 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061321 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061321/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061321 Building REAL250005061322 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061322' /scratch/stefan/7916143/working/building/REAL250005061322 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061322 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061322/0 /scratch/stefan/7916143/working/building/REAL250005061322 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/444 `/scratch/stefan/7916143/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005061322.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061322 none NC(=O)C(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 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 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [64, 45, 65, 45, 45, 10, 1, 1, 1, 1, 1, 7, 7, 38, 38, 38, 38, 38, 1, 1, 1, 64, 65, 45, 10, 10, 1, 1, 1, 38, 1, 1, 1, 1] 181 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 18, 19, 20, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 29]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061322 none NC(=O)C(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 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 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [181, 176, 181, 176, 176, 116, 38, 38, 38, 10, 1, 10, 1, 1, 1, 1, 1, 1, 38, 38, 38, 181, 181, 176, 116, 116, 38, 38, 38, 1, 38, 38, 38, 38] 181 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: 595 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061322 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061322 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061322/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061322 Building REAL250005061323 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061323' /scratch/stefan/7916143/working/building/REAL250005061323 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061323 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061323/0 /scratch/stefan/7916143/working/building/REAL250005061323 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/445 `/scratch/stefan/7916143/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005061323.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061323 none C=CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.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: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [129, 100, 28, 28, 28, 8, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 1, 129, 129, 129, 100, 100, 28, 8, 8, 1, 1, 1, 21, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 502 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061323 none C=CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.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: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 118, 118, 118, 63, 21, 21, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 201, 201, 201, 201, 201, 118, 63, 63, 21, 21, 21, 1, 21, 21, 21, 21] 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: 779 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061323 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061323 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061323/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061323 Building REAL250005061324 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061324' /scratch/stefan/7916143/working/building/REAL250005061324 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061324 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061324/0 /scratch/stefan/7916143/working/building/REAL250005061324 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/446 `/scratch/stefan/7916143/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005061324.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061324 none O=C(CO)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 534 conformations in input total number of sets (complete confs): 534 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 90, 10, 1, 1, 1, 1, 1, 7, 7, 39, 39, 39, 39, 39, 1, 1, 1, 91, 91, 273, 49, 10, 10, 1, 1, 1, 39, 1, 1, 1, 1] 534 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 17, 18, 19, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 665 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061324 none O=C(CO)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 534 conformations in input total number of sets (complete confs): 534 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 178, 129, 39, 39, 39, 11, 1, 11, 1, 1, 1, 1, 1, 1, 39, 39, 39, 178, 178, 534, 178, 129, 129, 39, 39, 39, 1, 39, 39, 39, 39] 534 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 1128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061324 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061324 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061324/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061324 Building REAL250005061325 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061325' /scratch/stefan/7916143/working/building/REAL250005061325 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061325 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061325/0 /scratch/stefan/7916143/working/building/REAL250005061325 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/447 `/scratch/stefan/7916143/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005061325.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061325 none CC(O)C(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 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', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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] 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: [104, 45, 101, 45, 45, 10, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 34, 1, 1, 1, 104, 104, 104, 104, 312, 45, 10, 10, 1, 1, 1, 34, 1, 1, 1, 1] 603 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061325 none CC(O)C(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 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', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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] 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, 191, 201, 191, 191, 122, 34, 34, 34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 34, 34, 201, 201, 201, 201, 603, 191, 122, 122, 34, 34, 34, 1, 34, 34, 34, 34] 603 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: 1287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061325 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061325 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061325/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061325 Building REAL250005061326 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061326' /scratch/stefan/7916143/working/building/REAL250005061326 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061326 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061326/0 /scratch/stefan/7916143/working/building/REAL250005061326 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/448 `/scratch/stefan/7916143/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005061326.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061326 none C[C@@H](O)C(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 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', '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, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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] 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: [104, 45, 104, 102, 45, 45, 10, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 1, 104, 104, 104, 312, 45, 10, 10, 1, 1, 1, 35, 1, 1, 1, 1] 603 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061326 none C[C@@H](O)C(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 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', '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, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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] 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, 191, 201, 201, 191, 191, 123, 35, 35, 35, 10, 1, 10, 1, 1, 1, 1, 1, 1, 35, 35, 35, 201, 201, 201, 603, 191, 123, 123, 35, 35, 35, 1, 35, 35, 35, 35] 603 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 1286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061326 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061326 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061326/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061326 Building REAL250005061327 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061327' /scratch/stefan/7916143/working/building/REAL250005061327 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061327 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061327/0 /scratch/stefan/7916143/working/building/REAL250005061327 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/449 `/scratch/stefan/7916143/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005061327.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061327 none C[C@H](O)C(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 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', '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, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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] 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: [103, 45, 103, 103, 45, 45, 9, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 1, 103, 103, 103, 309, 45, 9, 9, 1, 1, 1, 35, 1, 1, 1, 1] 603 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061327 none C[C@H](O)C(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 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', '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, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 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] 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, 191, 201, 201, 191, 191, 123, 35, 35, 35, 10, 1, 10, 1, 1, 1, 1, 1, 1, 35, 35, 35, 201, 201, 201, 603, 191, 123, 123, 35, 35, 35, 1, 35, 35, 35, 35] 603 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 1286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061327 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061327 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061327/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061327 Building REAL250005061328 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061328' /scratch/stefan/7916143/working/building/REAL250005061328 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061328 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061328/0 /scratch/stefan/7916143/working/building/REAL250005061328 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/450 `/scratch/stefan/7916143/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005061328.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061328 none CC=CC(=O)NCC1CN(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', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [97, 97, 42, 42, 42, 10, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 32, 1, 1, 1, 97, 97, 97, 97, 97, 42, 10, 10, 1, 1, 1, 32, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061328 none CC=CC(=O)NCC1CN(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', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 166, 166, 166, 109, 32, 32, 32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 32, 32, 32, 201, 201, 201, 201, 201, 166, 109, 109, 32, 32, 32, 1, 32, 32, 32, 32] 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: 681 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061328 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061328 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061328/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061328 Building REAL250005061329 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061329' /scratch/stefan/7916143/working/building/REAL250005061329 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061329 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061329/0 /scratch/stefan/7916143/working/building/REAL250005061329 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/451 `/scratch/stefan/7916143/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061329.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061329 none COCC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [45, 21, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 36, 36, 36, 48, 48, 48, 48, 48, 1, 45, 45, 45, 21, 21, 1, 1, 1, 1, 1, 9, 9, 36, 48, 1, 1] 133 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 35, 20, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 225 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061329 none COCC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 124, 80, 48, 80, 48, 48, 48, 48, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 48, 133, 133, 133, 124, 124, 48, 48, 48, 48, 48, 20, 20, 7, 1, 48, 48] 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, 35, 36]) total number of confs: 504 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061329 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061329 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061329/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061329 Building REAL250005061330 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061330' /scratch/stefan/7916143/working/building/REAL250005061330 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061330 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061330/0 /scratch/stefan/7916143/working/building/REAL250005061330 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/452 `/scratch/stefan/7916143/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061330.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061330 none CCCC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 23, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 52, 52, 52, 76, 76, 76, 76, 76, 1, 37, 38, 38, 37, 37, 23, 23, 1, 1, 1, 1, 1, 10, 10, 52, 76, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 37, 20, 38, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 355 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061330 none CCCC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 147, 76, 147, 76, 76, 76, 76, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 76, 201, 201, 201, 201, 201, 191, 191, 76, 76, 76, 76, 76, 28, 28, 8, 1, 76, 76] 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: 739 number of broken/clashed sets: 44 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061330 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061330 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061330/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061330 Building REAL250005061331 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061331' /scratch/stefan/7916143/working/building/REAL250005061331 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061331 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061331/0 /scratch/stefan/7916143/working/building/REAL250005061331 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/453 `/scratch/stefan/7916143/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061331.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061331 none CC(C)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 10, 45, 45, 45, 61, 61, 61, 61, 61, 1, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 10, 10, 45, 61, 1, 1] 117 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 37, 20, 38, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 206 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061331 none CC(C)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 115, 117, 61, 115, 61, 61, 61, 61, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 61, 117, 117, 117, 117, 117, 117, 117, 61, 61, 61, 61, 61, 25, 25, 7, 1, 61, 61] 117 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: 364 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061331 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061331 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061331/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061331 Building REAL250005061332 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061332' /scratch/stefan/7916143/working/building/REAL250005061332 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061332 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061332/0 /scratch/stefan/7916143/working/building/REAL250005061332 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/454 `/scratch/stefan/7916143/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061332.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061332 none CCC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 53, 53, 53, 71, 71, 71, 71, 71, 1, 18, 18, 18, 17, 17, 1, 1, 1, 1, 1, 10, 10, 53, 71, 1, 1] 105 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 34, 19, 25, 26, 27, 28, 29] set([0, 1, 3, 33, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 235 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061332 none CCC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 71, 105, 71, 71, 71, 71, 25, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 71, 105, 105, 105, 105, 105, 71, 71, 71, 71, 71, 24, 24, 6, 1, 71, 71] 105 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: 321 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061332 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061332 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061332/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061332 Building REAL250005061333 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061333' /scratch/stefan/7916143/working/building/REAL250005061333 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061333 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061333/0 /scratch/stefan/7916143/working/building/REAL250005061333 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/455 `/scratch/stefan/7916143/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061333.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061333 none CC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 43, 43, 43, 53, 53, 53, 53, 53, 1, 5, 5, 5, 1, 1, 1, 1, 1, 10, 10, 43, 53, 1, 1] 66 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 18, 22, 23, 24, 25, 26, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 27, 28, 29, 30]) total number of confs: 142 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061333 none CC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 53, 66, 53, 53, 53, 53, 25, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 53, 66, 66, 66, 53, 53, 53, 53, 53, 24, 24, 6, 1, 53, 53] 66 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 216 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061333 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061333 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061333/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061333 Building REAL250005061334 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061334' /scratch/stefan/7916143/working/building/REAL250005061334 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061334 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061334/0 /scratch/stefan/7916143/working/building/REAL250005061334 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/456 `/scratch/stefan/7916143/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1CN(C(=O)C2CC2)CCO1)C1=CC(=O)[N-]O1) `REAL250005061334.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061334 none O=C(NCC1CN(C(=O)C2CC2)CCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 9, 1, 1, 1, 1, 1, 7, 7, 17, 17, 1, 1, 1, 52, 68, 68, 68, 68, 68, 52, 9, 9, 1, 1, 1, 17, 17, 17, 17, 17, 1, 1, 1, 1, 68] 132 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 12, 13, 14, 35, 24, 25, 26] set([0, 1, 2, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 36]) total number of confs: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061334 none O=C(NCC1CN(C(=O)C2CC2)CCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 81, 17, 17, 17, 8, 1, 8, 1, 1, 1, 17, 17, 17, 128, 132, 132, 132, 132, 132, 128, 81, 81, 17, 17, 17, 1, 1, 1, 1, 1, 17, 17, 17, 17, 132] 132 rigid atoms, others: [7, 9, 10, 11, 27, 28, 29, 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, 32, 33, 34, 35, 36]) total number of confs: 444 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061334 none O=C(NCC1CN(C(=O)C2CC2)CCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 25, 68, 68, 68, 94, 94, 132, 132, 68, 68, 68, 1, 1, 1, 1, 1, 1, 6, 25, 25, 68, 68, 68, 132, 132, 132, 132, 132, 68, 68, 68, 68, 1] 132 rigid atoms, others: [1, 36, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 450 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061334 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061334 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061334/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061334 Building REAL250005061335 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061335' /scratch/stefan/7916143/working/building/REAL250005061335 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061335 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061335/0 /scratch/stefan/7916143/working/building/REAL250005061335 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/457 `/scratch/stefan/7916143/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061335.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061335 none NC(=O)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 4, 10, 1, 4, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 20, 20, 20, 20, 20, 1, 10, 10, 1, 1, 1, 1, 1, 7, 7, 15, 20, 1, 1] 29 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 20, 23, 24, 25, 26, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 28, 29, 30, 31]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061335 none NC(=O)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 21, 29, 20, 21, 20, 20, 20, 20, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 29, 29, 20, 20, 20, 20, 20, 14, 14, 8, 1, 20, 20] 29 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061335 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061335 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061335/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061335 Building REAL250005061336 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061336' /scratch/stefan/7916143/working/building/REAL250005061336 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061336 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061336/0 /scratch/stefan/7916143/working/building/REAL250005061336 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/458 `/scratch/stefan/7916143/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061336.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061336 none O=C(CO)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 17, 1, 1, 1, 1, 1, 1, 9, 34, 34, 34, 46, 46, 46, 46, 46, 1, 17, 17, 51, 1, 1, 1, 1, 1, 9, 9, 34, 46, 1, 1] 192 rigid atoms, others: [32, 1, 33, 4, 5, 6, 7, 8, 9, 19, 23, 24, 25, 26, 27] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 218 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061336 none O=C(CO)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [59, 46, 59, 64, 46, 46, 46, 46, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 46, 64, 64, 192, 46, 46, 46, 46, 46, 21, 21, 8, 1, 46, 46] 192 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 408 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061336 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061336 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061336/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061336 Building REAL250005061337 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061337' /scratch/stefan/7916143/working/building/REAL250005061337 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061337 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061337/0 /scratch/stefan/7916143/working/building/REAL250005061337 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/459 `/scratch/stefan/7916143/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061337.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061337 none CC(O)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 1, 5, 1, 1, 1, 1, 1, 1, 10, 25, 25, 25, 29, 29, 29, 29, 29, 1, 14, 14, 14, 14, 42, 1, 1, 1, 1, 1, 10, 10, 25, 29, 1, 1] 138 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 35, 20, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 176 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061337 none CC(O)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [46, 38, 46, 29, 38, 29, 29, 29, 29, 14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 29, 46, 46, 46, 46, 138, 29, 29, 29, 29, 29, 14, 14, 7, 1, 29, 29] 138 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 297 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061337 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061337 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061337/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061337 Building REAL250005061338 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061338' /scratch/stefan/7916143/working/building/REAL250005061338 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061338 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061338/0 /scratch/stefan/7916143/working/building/REAL250005061338 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/460 `/scratch/stefan/7916143/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061338.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061338 none CC(=O)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 11, 1, 4, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 22, 22, 22, 22, 22, 1, 11, 11, 11, 1, 1, 1, 1, 1, 7, 7, 20, 22, 1, 1] 33 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 10, 20, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 29, 30, 31]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061338 none CC(=O)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 24, 33, 22, 24, 22, 22, 22, 22, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 22, 33, 33, 33, 22, 22, 22, 22, 22, 11, 11, 5, 1, 22, 22] 33 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061338 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061338 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061338/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061338 Building REAL250005061339 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061339' /scratch/stefan/7916143/working/building/REAL250005061339 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061339 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061339/0 /scratch/stefan/7916143/working/building/REAL250005061339 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/461 `/scratch/stefan/7916143/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061339.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061339 none CC=CC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 53, 53, 53, 70, 70, 70, 70, 70, 1, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 10, 10, 53, 70, 1, 1] 122 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 35, 20, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061339 none CC=CC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 103, 70, 103, 70, 70, 70, 70, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 70, 122, 122, 122, 122, 122, 70, 70, 70, 70, 70, 26, 26, 6, 1, 70, 70] 122 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 388 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061339 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061339 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061339/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061339 Building REAL250005061340 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061340' /scratch/stefan/7916143/working/building/REAL250005061340 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061340 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061340/0 /scratch/stefan/7916143/working/building/REAL250005061340 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/462 `/scratch/stefan/7916143/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061340.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061340 none C[C@H](O)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 16, 1, 6, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 34, 34, 34, 34, 34, 1, 16, 16, 16, 48, 1, 1, 1, 1, 1, 9, 9, 28, 34, 1, 1] 162 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 21, 36, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 195 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061340 none C[C@H](O)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [54, 48, 54, 54, 34, 48, 34, 34, 34, 34, 16, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 34, 54, 54, 54, 162, 34, 34, 34, 34, 34, 16, 16, 6, 1, 34, 34] 162 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 346 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061340 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061340 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061340/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061340 Building REAL250005061341 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061341' /scratch/stefan/7916143/working/building/REAL250005061341 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061341 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061341/0 /scratch/stefan/7916143/working/building/REAL250005061341 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/463 `/scratch/stefan/7916143/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061341.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061341 none C=CCC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [67, 29, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 52, 52, 52, 78, 78, 78, 78, 78, 1, 67, 67, 67, 29, 29, 1, 1, 1, 1, 1, 10, 10, 52, 78, 1, 1] 195 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 35, 20, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 390 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061341 none C=CCC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 138, 78, 138, 78, 78, 78, 78, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 78, 195, 195, 195, 195, 195, 78, 78, 78, 78, 78, 25, 25, 7, 1, 78, 78] 195 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 734 number of broken/clashed sets: 91 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061341 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061341 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061341/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061341 Building REAL250005061342 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061342' /scratch/stefan/7916143/working/building/REAL250005061342 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061342 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061342/0 /scratch/stefan/7916143/working/building/REAL250005061342 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/464 `/scratch/stefan/7916143/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061342.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061342 none N#CCC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 36, 36, 36, 44, 44, 44, 44, 44, 1, 26, 26, 1, 1, 1, 1, 1, 10, 10, 36, 44, 1, 1] 109 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 20, 23, 24, 25, 26, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 28, 29, 30, 31]) total number of confs: 206 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061342 none N#CCC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 82, 44, 82, 44, 44, 44, 44, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 44, 109, 109, 44, 44, 44, 44, 44, 19, 19, 6, 1, 44, 44] 109 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 408 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061342 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061342 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061342/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061342 Building REAL250005061343 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061343' /scratch/stefan/7916143/working/building/REAL250005061343 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061343 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061343/0 /scratch/stefan/7916143/working/building/REAL250005061343 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/465 `/scratch/stefan/7916143/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061343.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061343 none C[C@@H](O)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 14, 1, 5, 1, 1, 1, 1, 1, 1, 10, 26, 26, 26, 29, 29, 29, 29, 29, 1, 14, 14, 14, 42, 1, 1, 1, 1, 1, 10, 10, 26, 29, 1, 1] 135 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 21, 36, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 176 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061343 none C[C@@H](O)C(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [45, 37, 45, 45, 29, 37, 29, 29, 29, 29, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 29, 45, 45, 45, 135, 29, 29, 29, 29, 29, 14, 14, 6, 1, 29, 29] 135 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 291 number of broken/clashed sets: 65 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061343 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061343 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061343/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061343 Building REAL250005061344 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061344' /scratch/stefan/7916143/working/building/REAL250005061344 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061344 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061344/0 /scratch/stefan/7916143/working/building/REAL250005061344 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/466 `/scratch/stefan/7916143/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061344.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061344 none C=CC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [27, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 62, 62, 62, 62, 62, 1, 27, 27, 27, 1, 1, 1, 1, 1, 10, 10, 50, 62, 1, 1] 87 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 19, 23, 24, 25, 26, 27] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 218 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061344 none C=CC(=O)N1CCOC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 62, 87, 62, 62, 62, 62, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 62, 87, 87, 87, 62, 62, 62, 62, 62, 24, 24, 7, 1, 62, 62] 87 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 272 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061344 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061344 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061344/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061344 Building REAL250005061345 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061345' /scratch/stefan/7916143/working/building/REAL250005061345 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061345 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061345/0 /scratch/stefan/7916143/working/building/REAL250005061345 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/467 `/scratch/stefan/7916143/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061345.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061345 none CCC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [48, 23, 23, 23, 8, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 16, 1, 1, 1, 1, 48, 48, 48, 48, 48, 23, 8, 8, 3, 16, 1, 1, 1, 1, 1, 1, 1, 1] 53 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 16, 17, 18, 19, 37, 30, 31] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061345 none CCC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 39, 39, 39, 31, 16, 10, 9, 1, 9, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 53, 53, 53, 53, 53, 39, 31, 31, 10, 1, 16, 16, 16, 16, 16, 16, 16, 16] 53 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061345 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061345 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061345/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061345 Building REAL250005061346 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061346' /scratch/stefan/7916143/working/building/REAL250005061346 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061346 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061346/0 /scratch/stefan/7916143/working/building/REAL250005061346 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/468 `/scratch/stefan/7916143/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061346.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061346 none CC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 8, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 1, 14, 14, 14, 14, 8, 8, 3, 13, 1, 1, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [32, 33, 34, 4, 5, 6, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061346 none CC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 13, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 19, 19, 19, 19, 19, 19, 9, 1, 13, 13, 13, 13, 13, 13, 13, 13] 19 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061346 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061346 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061346/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061346 Building REAL250005061347 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061347' /scratch/stefan/7916143/working/building/REAL250005061347 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061347 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061347/0 /scratch/stefan/7916143/working/building/REAL250005061347 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/469 `/scratch/stefan/7916143/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(CNC(=O)C2CC2)CCCC1)C1=CC(=O)[N-]O1) `REAL250005061347.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061347 none O=C(NC1(CNC(=O)C2CC2)CCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 3, 1, 1, 1, 8, 25, 25, 25, 62, 62, 1, 1, 1, 1, 3, 16, 16, 16, 16, 16, 3, 8, 8, 25, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 1, 1, 16] 75 rigid atoms, others: [32, 33, 2, 3, 4, 37, 11, 12, 13, 14, 34, 35, 36, 30, 31] set([0, 1, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061347 none O=C(NC1(CNC(=O)C2CC2)CCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [64, 64, 63, 39, 11, 11, 1, 11, 1, 1, 1, 63, 63, 63, 63, 64, 76, 76, 76, 76, 76, 64, 39, 39, 11, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 63, 63, 76] 76 rigid atoms, others: [6, 8, 9, 10, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 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: 236 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005061347 none O=C(NC1(CNC(=O)C2CC2)CCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 1, 8, 9, 16, 34, 49, 49, 49, 75, 75, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 9, 34, 34, 49, 75, 75, 75, 75, 75, 16, 16, 16, 16, 16, 16, 16, 16, 1] 75 rigid atoms, others: [1, 38, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 272 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061347 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061347 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061347/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061347 Building REAL250005061348 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061348' /scratch/stefan/7916143/working/building/REAL250005061348 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061348 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061348/0 /scratch/stefan/7916143/working/building/REAL250005061348 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/470 `/scratch/stefan/7916143/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061348.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061348 none COCC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [81, 74, 29, 29, 29, 7, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 1, 81, 81, 81, 74, 74, 29, 7, 7, 3, 13, 1, 1, 1, 1, 1, 1, 1, 1] 89 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 17, 18, 19, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061348 none COCC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 50, 50, 50, 26, 13, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 89, 89, 89, 89, 89, 50, 26, 26, 8, 1, 13, 13, 13, 13, 13, 13, 13, 13] 89 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 366 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061348 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061348 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061348/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061348 Building REAL250005061349 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061349' /scratch/stefan/7916143/working/building/REAL250005061349 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061349 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061349/0 /scratch/stefan/7916143/working/building/REAL250005061349 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/471 `/scratch/stefan/7916143/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061349.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061349 none CCCC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [103, 88, 28, 28, 28, 8, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 16, 1, 1, 1, 1, 108, 108, 108, 108, 108, 88, 88, 28, 8, 8, 3, 16, 1, 1, 1, 1, 1, 1, 1, 1] 122 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 39, 17, 18, 19, 20, 40, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 488 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061349 none CCCC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [122, 118, 68, 68, 68, 36, 16, 10, 9, 1, 9, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 122, 122, 122, 122, 122, 118, 118, 68, 36, 36, 10, 1, 16, 16, 16, 16, 16, 16, 16, 16] 122 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 516 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061349 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061349 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061349/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061349 Building REAL250005061350 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061350' /scratch/stefan/7916143/working/building/REAL250005061350 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061350 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061350/0 /scratch/stefan/7916143/working/building/REAL250005061350 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/472 `/scratch/stefan/7916143/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061350.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061350 none CC(C)C(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [66, 28, 66, 28, 28, 8, 1, 1, 1, 3, 3, 3, 19, 19, 19, 19, 19, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 28, 8, 8, 3, 19, 1, 1, 1, 1, 1, 1, 1, 1] 79 rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 39, 17, 18, 19, 20, 40, 38] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061350 none CC(C)C(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 66, 79, 66, 66, 42, 19, 11, 10, 1, 10, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 79, 79, 79, 79, 79, 79, 79, 66, 42, 42, 11, 1, 19, 19, 19, 19, 19, 19, 19, 19] 79 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061350 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061350 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061350/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061350 Building REAL250005061351 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061351' /scratch/stefan/7916143/working/building/REAL250005061351 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061351 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061351/0 /scratch/stefan/7916143/working/building/REAL250005061351 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/473 `/scratch/stefan/7916143/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061351.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061351 none NC(=O)C(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [30, 21, 30, 21, 21, 7, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 1, 1, 30, 30, 21, 7, 7, 3, 10, 1, 1, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061351 none NC(=O)C(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 30, 33, 30, 30, 19, 10, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 33, 33, 30, 19, 19, 8, 1, 10, 10, 10, 10, 10, 10, 10, 10] 33 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061351 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061351 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061351/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061351 Building REAL250005061352 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061352' /scratch/stefan/7916143/working/building/REAL250005061352 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061352 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061352/0 /scratch/stefan/7916143/working/building/REAL250005061352 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/474 `/scratch/stefan/7916143/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061352.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061352 none C=CCC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [96, 80, 26, 26, 26, 8, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 1, 1, 1, 1, 96, 96, 96, 80, 80, 26, 8, 8, 3, 15, 1, 1, 1, 1, 1, 1, 1, 1] 101 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 17, 18, 19, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061352 none C=CCC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 66, 66, 66, 33, 15, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 101, 101, 101, 101, 101, 66, 33, 33, 9, 1, 15, 15, 15, 15, 15, 15, 15, 15] 101 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 423 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061352 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061352 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061352/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061352 Building REAL250005061353 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061353' /scratch/stefan/7916143/working/building/REAL250005061353 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061353 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061353/0 /scratch/stefan/7916143/working/building/REAL250005061353 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/475 `/scratch/stefan/7916143/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061353.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061353 none O=C(CO)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 25, 7, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 1, 25, 25, 75, 18, 7, 7, 3, 13, 1, 1, 1, 1, 1, 1, 1, 1] 81 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061353 none O=C(CO)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 27, 19, 13, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 27, 27, 81, 26, 19, 19, 7, 1, 13, 13, 13, 13, 13, 13, 13, 13] 81 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 182 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061353 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061353 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061353/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061353 Building REAL250005061354 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061354' /scratch/stefan/7916143/working/building/REAL250005061354 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061354 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061354/0 /scratch/stefan/7916143/working/building/REAL250005061354 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/476 `/scratch/stefan/7916143/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061354.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061354 none CC(O)C(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [48, 27, 48, 27, 27, 8, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 1, 1, 48, 48, 48, 48, 144, 27, 8, 8, 3, 14, 1, 1, 1, 1, 1, 1, 1, 1] 162 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 17, 18, 19, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061354 none CC(O)C(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [54, 47, 54, 47, 47, 27, 14, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 54, 54, 54, 54, 162, 47, 27, 27, 8, 1, 14, 14, 14, 14, 14, 14, 14, 14] 162 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 376 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061354 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061354 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061354/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061354 Building REAL250005061355 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061355' /scratch/stefan/7916143/working/building/REAL250005061355 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061355 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061355/0 /scratch/stefan/7916143/working/building/REAL250005061355 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/477 `/scratch/stefan/7916143/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061355.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061355 none O=C(CCF)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 27, 88, 96, 8, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 1, 1, 88, 88, 96, 96, 27, 8, 8, 3, 14, 1, 1, 1, 1, 1, 1, 1, 1] 101 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061355 none O=C(CCF)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [63, 63, 63, 101, 101, 31, 14, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 101, 101, 101, 101, 63, 31, 31, 8, 1, 14, 14, 14, 14, 14, 14, 14, 14] 101 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 406 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061355 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061355 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061355/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061355 Building REAL250005061356 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061356' /scratch/stefan/7916143/working/building/REAL250005061356 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061356 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061356/0 /scratch/stefan/7916143/working/building/REAL250005061356 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/478 `/scratch/stefan/7916143/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061356.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061356 none C[C@@H](O)C(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [48, 27, 48, 48, 27, 27, 8, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 1, 1, 48, 48, 48, 144, 27, 8, 8, 3, 14, 1, 1, 1, 1, 1, 1, 1, 1] 162 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061356 none C[C@@H](O)C(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [54, 47, 54, 54, 47, 47, 27, 14, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 54, 54, 54, 162, 47, 27, 27, 8, 1, 14, 14, 14, 14, 14, 14, 14, 14] 162 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 376 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061356 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061356 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061356/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061356 Building REAL250005061357 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061357' /scratch/stefan/7916143/working/building/REAL250005061357 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061357 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061357/0 /scratch/stefan/7916143/working/building/REAL250005061357 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/479 `/scratch/stefan/7916143/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061357.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061357 none C[C@H](O)C(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [38, 22, 38, 38, 22, 22, 8, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 1, 1, 38, 38, 38, 114, 22, 8, 8, 3, 14, 1, 1, 1, 1, 1, 1, 1, 1] 135 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061357 none C[C@H](O)C(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [45, 42, 45, 45, 42, 42, 26, 14, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 45, 45, 45, 135, 42, 26, 26, 8, 1, 14, 14, 14, 14, 14, 14, 14, 14] 135 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061357 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061357 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061357/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061357 Building REAL250005061358 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061358' /scratch/stefan/7916143/working/building/REAL250005061358 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061358 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061358/0 /scratch/stefan/7916143/working/building/REAL250005061358 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/480 `/scratch/stefan/7916143/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061358.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061358 none CC=CC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 22, 22, 22, 8, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 1, 35, 35, 35, 35, 35, 22, 8, 8, 3, 13, 1, 1, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 17, 18, 19, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061358 none CC=CC(=O)NCC1(NC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 33, 33, 33, 25, 13, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 41, 41, 41, 41, 41, 33, 25, 25, 9, 1, 13, 13, 13, 13, 13, 13, 13, 13] 41 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 152 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061358 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061358 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061358/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061358 Building REAL250005061359 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061359' /scratch/stefan/7916143/working/building/REAL250005061359 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061359 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061359/0 /scratch/stefan/7916143/working/building/REAL250005061359 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/481 `/scratch/stefan/7916143/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061359.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061359 none COCC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [42, 22, 3, 3, 3, 1, 1, 1, 9, 33, 33, 33, 46, 46, 46, 46, 46, 1, 1, 1, 1, 42, 42, 42, 22, 22, 3, 9, 9, 33, 46, 1, 1, 1, 1, 1, 1, 1, 1] 92 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 17, 18, 19, 20, 38, 37, 31] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061359 none COCC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 46, 46, 46, 46, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 92, 92, 92, 92, 92, 46, 21, 21, 7, 1, 46, 46, 46, 46, 46, 46, 46, 46] 92 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 350 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061359 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061359 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061359/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061359 Building REAL250005061360 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061360' /scratch/stefan/7916143/working/building/REAL250005061360 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061360 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061360/0 /scratch/stefan/7916143/working/building/REAL250005061360 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/482 `/scratch/stefan/7916143/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061360.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061360 none CCCC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [32, 19, 3, 3, 3, 1, 1, 1, 10, 40, 40, 40, 80, 80, 80, 80, 80, 1, 1, 1, 1, 39, 39, 39, 39, 39, 19, 19, 3, 10, 10, 40, 80, 1, 1, 1, 1, 1, 1, 1, 1] 152 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 40, 39, 17, 18, 19, 20, 38, 37] set([0, 1, 2, 3, 4, 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: 366 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061360 none CCCC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [152, 146, 81, 81, 81, 80, 44, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 152, 152, 152, 152, 152, 146, 146, 81, 44, 44, 12, 1, 80, 80, 80, 80, 80, 80, 80, 80] 152 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 593 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061360 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061360 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061360/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061360 Building REAL250005061361 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061361' /scratch/stefan/7916143/working/building/REAL250005061361 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061361 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061361/0 /scratch/stefan/7916143/working/building/REAL250005061361 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/483 `/scratch/stefan/7916143/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061361.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061361 none CC(C)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [18, 3, 18, 3, 3, 1, 1, 1, 9, 35, 35, 35, 52, 52, 52, 52, 52, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 3, 9, 9, 35, 52, 1, 1, 1, 1, 1, 1, 1, 1] 68 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 40, 39, 17, 18, 19, 20, 38, 37] set([0, 1, 2, 3, 4, 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061361 none CC(C)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 53, 68, 53, 53, 52, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 68, 68, 68, 68, 68, 68, 68, 53, 25, 25, 7, 1, 52, 52, 52, 52, 52, 52, 52, 52] 68 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061361 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061361 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061361/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061361 Building REAL250005061362 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061362' /scratch/stefan/7916143/working/building/REAL250005061362 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061362 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061362/0 /scratch/stefan/7916143/working/building/REAL250005061362 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/484 `/scratch/stefan/7916143/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061362.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061362 none CCC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [22, 3, 3, 3, 1, 1, 1, 9, 30, 30, 30, 45, 45, 45, 45, 45, 1, 1, 1, 1, 22, 22, 22, 22, 22, 3, 9, 9, 30, 45, 1, 1, 1, 1, 1, 1, 1, 1] 69 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 16, 17, 18, 19, 36, 37, 30, 31] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061362 none CCC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 46, 46, 46, 45, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 69, 69, 69, 69, 69, 46, 29, 29, 9, 1, 45, 45, 45, 45, 45, 45, 45, 45] 69 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061362 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061362 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061362/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061362 Building REAL250005061363 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061363' /scratch/stefan/7916143/working/building/REAL250005061363 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061363 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061363/0 /scratch/stefan/7916143/working/building/REAL250005061363 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/485 `/scratch/stefan/7916143/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061363.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061363 none CC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 9, 18, 18, 18, 22, 22, 22, 22, 22, 1, 1, 1, 1, 3, 3, 3, 3, 9, 9, 18, 22, 1, 1, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [32, 33, 34, 3, 4, 5, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061363 none CC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 22, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 23, 23, 23, 23, 14, 14, 4, 1, 22, 22, 22, 22, 22, 22, 22, 22] 23 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061363 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061363 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061363/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061363 Building REAL250005061364 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061364' /scratch/stefan/7916143/working/building/REAL250005061364 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061364 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061364/0 /scratch/stefan/7916143/working/building/REAL250005061364 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/486 `/scratch/stefan/7916143/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(NC(=O)C2CC2)CCCC1)C1=CC(=O)[N-]O1) `REAL250005061364.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061364 none O=C(NCC1(NC(=O)C2CC2)CCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 9, 1, 1, 1, 3, 3, 3, 20, 20, 1, 1, 1, 1, 30, 48, 48, 48, 48, 48, 30, 9, 9, 3, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 48] 88 rigid atoms, others: [32, 33, 34, 3, 4, 5, 11, 12, 13, 14, 35, 36, 37, 30, 31] set([0, 1, 2, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061364 none O=C(NCC1(NC(=O)C2CC2)CCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 53, 20, 13, 13, 1, 13, 1, 1, 1, 20, 20, 20, 20, 78, 88, 88, 88, 88, 88, 78, 53, 53, 13, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 88] 88 rigid atoms, others: [6, 8, 9, 10, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 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: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005061364 none O=C(NCC1(NC(=O)C2CC2)CCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 26, 47, 48, 48, 48, 88, 88, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 8, 26, 26, 48, 88, 88, 88, 88, 88, 47, 47, 47, 47, 47, 47, 47, 47, 1] 88 rigid atoms, others: [1, 38, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 283 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061364 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061364 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061364/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061364 Building REAL250005061365 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061365' /scratch/stefan/7916143/working/building/REAL250005061365 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061365 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061365/0 /scratch/stefan/7916143/working/building/REAL250005061365 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/487 `/scratch/stefan/7916143/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061365.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061365 none NC(=O)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 3, 12, 3, 3, 1, 1, 1, 8, 26, 26, 26, 31, 31, 31, 31, 31, 1, 1, 1, 1, 12, 12, 3, 8, 8, 26, 31, 1, 1, 1, 1, 1, 1, 1, 1] 40 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061365 none NC(=O)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 33, 40, 33, 33, 31, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 40, 40, 33, 17, 17, 5, 1, 31, 31, 31, 31, 31, 31, 31, 31] 40 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061365 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061365 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061365/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061365 Building REAL250005061366 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061366' /scratch/stefan/7916143/working/building/REAL250005061366 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061366 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061366/0 /scratch/stefan/7916143/working/building/REAL250005061366 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/488 `/scratch/stefan/7916143/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061366.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061366 none O=C(CO)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 18, 1, 1, 1, 9, 24, 24, 24, 35, 35, 35, 35, 35, 1, 1, 1, 1, 18, 18, 54, 3, 9, 9, 24, 35, 1, 1, 1, 1, 1, 1, 1, 1] 123 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061366 none O=C(CO)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 41, 35, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 41, 41, 123, 36, 21, 21, 7, 1, 35, 35, 35, 35, 35, 35, 35, 35] 123 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061366 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061366 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061366/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061366 Building REAL250005061367 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061367' /scratch/stefan/7916143/working/building/REAL250005061367 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061367 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061367/0 /scratch/stefan/7916143/working/building/REAL250005061367 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/489 `/scratch/stefan/7916143/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061367.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061367 none CC(O)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [16, 3, 16, 3, 3, 1, 1, 1, 8, 27, 27, 27, 37, 37, 37, 37, 37, 1, 1, 1, 1, 16, 16, 16, 16, 48, 3, 8, 8, 27, 37, 1, 1, 1, 1, 1, 1, 1, 1] 141 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 17, 18, 19, 20, 38, 37, 31] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061367 none CC(O)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [47, 38, 47, 38, 38, 37, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 47, 47, 47, 47, 141, 38, 21, 21, 8, 1, 37, 37, 37, 37, 37, 37, 37, 37] 141 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061367 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061367 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061367/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061367 Building REAL250005061368 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061368' /scratch/stefan/7916143/working/building/REAL250005061368 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061368 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061368/0 /scratch/stefan/7916143/working/building/REAL250005061368 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/490 `/scratch/stefan/7916143/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061368.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061368 none CC(=O)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 3, 13, 3, 3, 1, 1, 1, 8, 25, 25, 25, 34, 34, 34, 34, 34, 1, 1, 1, 1, 13, 13, 13, 3, 8, 8, 25, 34, 1, 1, 1, 1, 1, 1, 1, 1] 45 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061368 none CC(=O)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 36, 45, 36, 36, 34, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 45, 45, 45, 36, 21, 21, 8, 1, 34, 34, 34, 34, 34, 34, 34, 34] 45 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061368 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061368 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061368/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061368 Building REAL250005061369 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061369' /scratch/stefan/7916143/working/building/REAL250005061369 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061369 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061369/0 /scratch/stefan/7916143/working/building/REAL250005061369 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/491 `/scratch/stefan/7916143/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061369.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061369 none CC=CC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 3, 3, 3, 1, 1, 1, 8, 28, 28, 28, 41, 41, 41, 41, 41, 1, 1, 1, 1, 16, 16, 16, 16, 16, 3, 8, 8, 28, 41, 1, 1, 1, 1, 1, 1, 1, 1] 57 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 17, 18, 19, 20, 38, 37, 31] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061369 none CC=CC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 42, 42, 42, 41, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 57, 57, 57, 57, 57, 42, 24, 24, 9, 1, 41, 41, 41, 41, 41, 41, 41, 41] 57 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 196 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061369 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061369 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061369/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061369 Building REAL250005061370 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061370' /scratch/stefan/7916143/working/building/REAL250005061370 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061370 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061370/0 /scratch/stefan/7916143/working/building/REAL250005061370 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/492 `/scratch/stefan/7916143/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061370.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061370 none C[C@H](O)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [16, 3, 16, 16, 3, 3, 1, 1, 1, 9, 30, 30, 30, 41, 41, 41, 41, 41, 1, 1, 1, 1, 16, 16, 16, 48, 3, 9, 9, 30, 41, 1, 1, 1, 1, 1, 1, 1, 1] 153 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 18, 19, 20, 21, 38, 31] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061370 none C[C@H](O)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [51, 43, 51, 51, 43, 43, 41, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 51, 51, 51, 153, 43, 23, 23, 8, 1, 41, 41, 41, 41, 41, 41, 41, 41] 153 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 328 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061370 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061370 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061370/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061370 Building REAL250005061371 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061371' /scratch/stefan/7916143/working/building/REAL250005061371 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061371 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061371/0 /scratch/stefan/7916143/working/building/REAL250005061371 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/493 `/scratch/stefan/7916143/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061371.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061371 none C=CCC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [59, 25, 3, 3, 3, 1, 1, 1, 10, 39, 39, 39, 72, 72, 72, 72, 72, 1, 1, 1, 1, 59, 59, 59, 25, 25, 3, 10, 10, 39, 72, 1, 1, 1, 1, 1, 1, 1, 1] 141 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 17, 18, 19, 20, 38, 37, 31] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061371 none C=CCC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 73, 73, 73, 72, 35, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 141, 141, 141, 141, 141, 73, 35, 35, 10, 1, 72, 72, 72, 72, 72, 72, 72, 72] 141 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 539 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061371 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061371 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061371/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061371 Building REAL250005061372 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061372' /scratch/stefan/7916143/working/building/REAL250005061372 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061372 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061372/0 /scratch/stefan/7916143/working/building/REAL250005061372 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/494 `/scratch/stefan/7916143/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061372.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061372 none N#CCC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 3, 3, 3, 1, 1, 1, 9, 31, 31, 31, 42, 42, 42, 42, 42, 1, 1, 1, 1, 23, 23, 3, 9, 9, 31, 42, 1, 1, 1, 1, 1, 1, 1, 1] 69 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061372 none N#CCC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 42, 42, 42, 42, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 69, 69, 42, 18, 18, 7, 1, 42, 42, 42, 42, 42, 42, 42, 42] 69 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061372 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061372 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061372/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061372 Building REAL250005061373 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061373' /scratch/stefan/7916143/working/building/REAL250005061373 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061373 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061373/0 /scratch/stefan/7916143/working/building/REAL250005061373 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/495 `/scratch/stefan/7916143/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061373.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061373 none O=C(CCF)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 19, 44, 1, 1, 1, 9, 36, 36, 36, 64, 64, 64, 64, 64, 1, 1, 1, 1, 19, 19, 44, 44, 3, 9, 9, 36, 64, 1, 1, 1, 1, 1, 1, 1, 1] 138 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 17, 18, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061373 none O=C(CCF)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [65, 65, 65, 138, 138, 64, 32, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 138, 138, 138, 138, 65, 32, 32, 8, 1, 64, 64, 64, 64, 64, 64, 64, 64] 138 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 541 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061373 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061373 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061373/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061373 Building REAL250005061374 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061374' /scratch/stefan/7916143/working/building/REAL250005061374 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061374 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061374/0 /scratch/stefan/7916143/working/building/REAL250005061374 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/496 `/scratch/stefan/7916143/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061374.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061374 none C[C@@H](O)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [16, 3, 16, 16, 3, 3, 1, 1, 1, 8, 27, 27, 27, 37, 37, 37, 37, 37, 1, 1, 1, 1, 16, 16, 16, 48, 3, 8, 8, 27, 37, 1, 1, 1, 1, 1, 1, 1, 1] 141 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 18, 19, 20, 21, 38, 31] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061374 none C[C@@H](O)C(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [47, 38, 47, 47, 38, 38, 37, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 47, 47, 47, 141, 38, 21, 21, 8, 1, 37, 37, 37, 37, 37, 37, 37, 37] 141 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061374 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061374 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061374/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061374 Building REAL250005061375 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061375' /scratch/stefan/7916143/working/building/REAL250005061375 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061375 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061375/0 /scratch/stefan/7916143/working/building/REAL250005061375 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/497 `/scratch/stefan/7916143/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005061375.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061375 none C=CC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 3, 3, 1, 1, 1, 8, 27, 27, 27, 41, 41, 41, 41, 41, 1, 1, 1, 1, 11, 11, 11, 3, 8, 8, 27, 41, 1, 1, 1, 1, 1, 1, 1, 1] 42 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061375 none C=CC(=O)NC1(CNC(=O)C2=CC(=O)[N-]O2)CCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 41, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 42, 42, 42, 42, 25, 25, 7, 1, 41, 41, 41, 41, 41, 41, 41, 41] 42 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061375 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061375 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061375/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061375 Building REAL250005061376 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061376' /scratch/stefan/7916143/working/building/REAL250005061376 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061376 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061376/0 /scratch/stefan/7916143/working/building/REAL250005061376 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/498 `/scratch/stefan/7916143/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1) `REAL250005061376.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061376 none CCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 16, 16, 16, 15, 15, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38] set([0, 1, 3, 32, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25]) total number of confs: 86 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061376 none CCC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 15, 41, 15, 15, 15, 15, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 41, 41, 41, 41, 41, 15, 15, 15, 15, 14, 14, 1, 15, 15, 15, 15, 15, 15] 41 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: 97 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061376 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061376 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061376/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061376 Building REAL250005061377 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061377' /scratch/stefan/7916143/working/building/REAL250005061377 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061377 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061377/0 /scratch/stefan/7916143/working/building/REAL250005061377 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/499 `/scratch/stefan/7916143/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1) `REAL250005061377.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061377 none CC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 29]) total number of confs: 39 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061377 none CC(=O)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 23, 17, 17, 17, 17, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 23, 23, 23, 17, 17, 17, 17, 16, 16, 1, 17, 17, 17, 17, 17, 17] 23 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 55 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061377 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061377 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061377/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061377 Building REAL250005061378 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061378' /scratch/stefan/7916143/working/building/REAL250005061378 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061378 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061378/0 /scratch/stefan/7916143/working/building/REAL250005061378 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/500 `/scratch/stefan/7916143/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1) `REAL250005061378.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061378 none O=C(CO)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 20, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 20, 20, 60, 1, 1, 1, 1, 1, 1, 26, 1, 1, 1, 1, 1, 1] 174 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 30]) total number of confs: 171 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061378 none O=C(CO)N1CCC2(CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [56, 26, 56, 58, 26, 26, 26, 26, 25, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 26, 26, 58, 58, 174, 26, 26, 26, 26, 26, 25, 1, 26, 26, 26, 26, 26, 26] 174 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: 327 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061378 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061378 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061378/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061378 Building REAL250005061379 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061379' /scratch/stefan/7916143/working/building/REAL250005061379 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061379 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061379/0 /scratch/stefan/7916143/working/building/REAL250005061379 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/501 `/scratch/stefan/7916143/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)CC2) `REAL250005061379.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061379 none CCC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 31, 1, 1, 1, 1] 68 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38] set([0, 1, 34, 3, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061379 none CCC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 56, 31, 56, 31, 31, 31, 31, 31, 31, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 31, 68, 68, 68, 68, 68, 31, 31, 31, 31, 31, 31, 31, 31, 1, 31, 31, 31, 31] 68 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: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061379 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061379 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061379/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061379 Building REAL250005061380 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061380' /scratch/stefan/7916143/working/building/REAL250005061380 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061380 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061380/0 /scratch/stefan/7916143/working/building/REAL250005061380 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/502 `/scratch/stefan/7916143/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)CC2) `REAL250005061380.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061380 none CC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1] 22 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061380 none CC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 12, 22, 12, 12, 12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 22, 22, 22, 12, 12, 12, 12, 12, 12, 12, 12, 1, 12, 12, 12, 12] 22 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: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061380 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061380 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061380/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061380 Building REAL250005061381 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061381' /scratch/stefan/7916143/working/building/REAL250005061381 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061381 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061381/0 /scratch/stefan/7916143/working/building/REAL250005061381 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/503 `/scratch/stefan/7916143/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)CC2) `REAL250005061381.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061381 none O=C(CO)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 21, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 21, 21, 63, 1, 1, 1, 1, 1, 1, 1, 1, 33, 1, 1, 1, 1] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36] set([0, 32, 2, 3, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23]) total number of confs: 176 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061381 none O=C(CO)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)CC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 33, 54, 67, 33, 33, 33, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 67, 67, 201, 33, 33, 33, 33, 33, 33, 33, 33, 1, 33, 33, 33, 33] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 410 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061381 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061381 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061381/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061381 Building REAL250005061382 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061382' /scratch/stefan/7916143/working/building/REAL250005061382 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061382 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061382/0 /scratch/stefan/7916143/working/building/REAL250005061382 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/504 `/scratch/stefan/7916143/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)CC2) `REAL250005061382.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061382 none C=CC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)CC2 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 26, 1, 1, 1, 1] 53 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36] set([0, 1, 3, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061382 none C=CC(=O)N1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)CC2 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 26, 53, 26, 26, 26, 26, 26, 26, 12, 1, 12, 1, 1, 1, 1, 1, 1, 26, 26, 53, 53, 53, 26, 26, 26, 26, 26, 26, 26, 26, 1, 26, 26, 26, 26] 53 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061382 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061382 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061382/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061382 Building REAL250005061383 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061383' /scratch/stefan/7916143/working/building/REAL250005061383 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061383 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061383/0 /scratch/stefan/7916143/working/building/REAL250005061383 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/505 `/scratch/stefan/7916143/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061383.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061383 none CCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [163, 152, 123, 152, 94, 123, 39, 92, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 163, 123, 123, 123, 94, 94, 94, 94, 39, 39, 9, 1] 163 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: 645 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061383 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061383 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061383/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061383 Building REAL250005061384 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061384' /scratch/stefan/7916143/working/building/REAL250005061384 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061384 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061384/0 /scratch/stefan/7916143/working/building/REAL250005061384 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/506 `/scratch/stefan/7916143/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061384.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061384 none COCCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 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, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 191, 151, 88, 151, 66, 88, 21, 62, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 199, 199, 191, 191, 88, 88, 88, 66, 66, 66, 66, 21, 21, 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: 786 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061384 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061384 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061384/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061384 Building REAL250005061385 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061385' /scratch/stefan/7916143/working/building/REAL250005061385 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061385 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061385/0 /scratch/stefan/7916143/working/building/REAL250005061385 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/507 `/scratch/stefan/7916143/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC1) `REAL250005061385.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061385 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 83, 127, 127, 159, 159, 201, 201, 83, 83, 83, 83, 28, 28, 7, 1, 127, 127, 127, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 26] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 757 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061385 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 55, 131, 199, 199, 199, 201, 201, 201, 201, 201, 8, 24, 1, 8, 1, 1, 1, 55, 55, 55, 55, 131, 131, 199, 201, 24, 24, 24, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 762 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061385 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061385 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061385/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061385 Building REAL250005061386 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061386' /scratch/stefan/7916143/working/building/REAL250005061386 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061386 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061386/0 /scratch/stefan/7916143/working/building/REAL250005061386 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/508 `/scratch/stefan/7916143/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCC1) `REAL250005061386.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061386 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 81, 121, 121, 164, 164, 201, 201, 201, 81, 81, 81, 81, 25, 25, 5, 1, 121, 121, 121, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 751 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061386 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 62, 139, 200, 200, 200, 201, 201, 201, 201, 201, 8, 24, 1, 8, 1, 1, 1, 1, 62, 62, 62, 62, 139, 139, 200, 201, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 789 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061386 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061386 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061386/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061386 Building REAL250005061387 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061387' /scratch/stefan/7916143/working/building/REAL250005061387 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061387 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061387/0 /scratch/stefan/7916143/working/building/REAL250005061387 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/509 `/scratch/stefan/7916143/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCCC1) `REAL250005061387.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061387 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 107, 107, 177, 177, 201, 201, 201, 201, 65, 65, 65, 65, 24, 24, 4, 1, 107, 107, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 716 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061387 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 62, 138, 201, 201, 201, 201, 201, 201, 201, 201, 6, 22, 1, 6, 1, 1, 1, 1, 1, 62, 62, 62, 62, 138, 138, 201, 201, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 798 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061387 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061387 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061387/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061387 Building REAL250005061388 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061388' /scratch/stefan/7916143/working/building/REAL250005061388 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061388 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061388/0 /scratch/stefan/7916143/working/building/REAL250005061388 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/510 `/scratch/stefan/7916143/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC1CC1) `REAL250005061388.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061388 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 61, 95, 94, 144, 144, 156, 201, 201, 61, 61, 61, 61, 23, 23, 4, 1, 95, 95, 95, 156, 156, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 772 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061388 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 65, 136, 201, 201, 201, 201, 201, 201, 201, 201, 14, 35, 3, 14, 1, 1, 1, 1, 65, 65, 65, 65, 136, 136, 201, 201, 35, 35, 35, 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: 774 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061388 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061388 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061388/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061388 Building REAL250005061389 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061389' /scratch/stefan/7916143/working/building/REAL250005061389 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061389 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061389/0 /scratch/stefan/7916143/working/building/REAL250005061389 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/511 `/scratch/stefan/7916143/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(C)(C)F) `REAL250005061389.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061389 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 13, 14, 14, 14, 12, 12, 12, 12, 8, 8, 2, 1, 13, 13, 13, 14, 14, 14, 14, 14, 14] 14 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 61 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061389 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061389 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061389/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061389 Building REAL250005061390 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061390' /scratch/stefan/7916143/working/building/REAL250005061390 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061390 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061390/0 /scratch/stefan/7916143/working/building/REAL250005061390 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/512 `/scratch/stefan/7916143/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(C)(F)F) `REAL250005061390.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061390 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(C)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061390 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061390 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061390/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061390 Building REAL250005061391 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061391' /scratch/stefan/7916143/working/building/REAL250005061391 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061391 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061391/0 /scratch/stefan/7916143/working/building/REAL250005061391 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/513 `/scratch/stefan/7916143/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061391.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061391 none COCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 127, 88, 127, 69, 88, 28, 67, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 198, 198, 88, 88, 88, 69, 69, 69, 69, 28, 28, 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: 845 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061391 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061391 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061391/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061391 Building REAL250005061392 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061392' /scratch/stefan/7916143/working/building/REAL250005061392 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061392 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061392/0 /scratch/stefan/7916143/working/building/REAL250005061392 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/514 `/scratch/stefan/7916143/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061392.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061392 none CCCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 127, 84, 127, 57, 84, 22, 54, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 194, 194, 84, 84, 84, 57, 57, 57, 57, 22, 22, 6, 1] 201 rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 826 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061392 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061392 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061392/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061392 Building REAL250005061393 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061393' /scratch/stefan/7916143/working/building/REAL250005061393 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061393 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061393/0 /scratch/stefan/7916143/working/building/REAL250005061393 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/515 `/scratch/stefan/7916143/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CC=CO1) `REAL250005061393.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061393 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [59, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 60, 95, 95, 154, 154, 187, 187, 187, 187, 60, 60, 60, 60, 18, 18, 4, 1, 95, 95, 95, 187, 187, 187] 187 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 587 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061393 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [77, 36, 77, 136, 187, 187, 187, 187, 187, 187, 187, 187, 12, 36, 1, 12, 1, 1, 1, 1, 1, 77, 77, 77, 77, 136, 136, 187, 187, 36, 36, 36, 1, 1, 1] 187 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 748 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061393 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061393 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061393/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061393 Building REAL250005061394 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061394' /scratch/stefan/7916143/working/building/REAL250005061394 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061394 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061394/0 /scratch/stefan/7916143/working/building/REAL250005061394 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/516 `/scratch/stefan/7916143/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061394.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061394 none CC(=O)NCC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 186, 139, 86, 139, 65, 86, 19, 62, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 186, 186, 86, 86, 86, 65, 65, 65, 65, 19, 19, 5, 1] 199 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: 775 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061394 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061394 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061394/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061394 Building REAL250005061395 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061395' /scratch/stefan/7916143/working/building/REAL250005061395 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061395 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061395/0 /scratch/stefan/7916143/working/building/REAL250005061395 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/517 `/scratch/stefan/7916143/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061395.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061395 none CC(C)CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 146, 101, 146, 76, 101, 31, 73, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 101, 101, 76, 76, 76, 76, 31, 31, 8, 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: 827 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061395 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061395 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061395/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061395 Building REAL250005061396 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061396' /scratch/stefan/7916143/working/building/REAL250005061396 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061396 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061396/0 /scratch/stefan/7916143/working/building/REAL250005061396 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/518 `/scratch/stefan/7916143/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC1C) `REAL250005061396.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061396 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 24, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 72, 111, 111, 165, 165, 201, 201, 201, 72, 72, 72, 72, 24, 24, 5, 1, 111, 111, 111, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 741 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061396 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 72, 144, 200, 200, 200, 201, 201, 201, 201, 201, 8, 27, 1, 8, 1, 1, 1, 1, 72, 72, 72, 72, 144, 144, 200, 201, 27, 27, 27, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 790 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061396 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061396 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061396/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061396 Building REAL250005061397 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061397' /scratch/stefan/7916143/working/building/REAL250005061397 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061397 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061397/0 /scratch/stefan/7916143/working/building/REAL250005061397 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/519 `/scratch/stefan/7916143/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061397.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061397 none CCOCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 172, 115, 69, 115, 53, 69, 21, 52, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 172, 172, 69, 69, 69, 53, 53, 53, 53, 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: 776 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061397 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061397 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061397/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061397 Building REAL250005061398 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061398' /scratch/stefan/7916143/working/building/REAL250005061398 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061398 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061398/0 /scratch/stefan/7916143/working/building/REAL250005061398 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/520 `/scratch/stefan/7916143/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061398.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061398 none CC(C)=CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 110, 89, 110, 73, 89, 39, 72, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 132, 132, 132, 89, 89, 89, 73, 73, 73, 73, 39, 39, 11, 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: 521 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061398 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061398 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061398/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061398 Building REAL250005061399 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061399' /scratch/stefan/7916143/working/building/REAL250005061399 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061399 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061399/0 /scratch/stefan/7916143/working/building/REAL250005061399 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/521 `/scratch/stefan/7916143/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCCO1) `REAL250005061399.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061399 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 12, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 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: [35, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 52, 51, 61, 61, 68, 68, 68, 68, 35, 35, 35, 35, 17, 17, 4, 1, 52, 52, 52, 68, 68, 68, 68, 68, 68, 68] 68 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 258 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061399 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 12, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 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: [36, 22, 36, 56, 68, 68, 68, 68, 68, 68, 68, 68, 7, 22, 1, 7, 1, 1, 1, 1, 1, 36, 36, 36, 36, 56, 56, 68, 68, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1] 68 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 260 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061399 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061399 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061399/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061399 Building REAL250005061400 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061400' /scratch/stefan/7916143/working/building/REAL250005061400 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061400 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061400/0 /scratch/stefan/7916143/working/building/REAL250005061400 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/522 `/scratch/stefan/7916143/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061400.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061400 none CSCC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 104, 65, 104, 49, 65, 19, 47, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 171, 171, 65, 65, 65, 49, 49, 49, 49, 19, 19, 5, 1] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 799 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061400 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061400 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061400/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061400 Building REAL250005061401 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061401' /scratch/stefan/7916143/working/building/REAL250005061401 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061401 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061401/0 /scratch/stefan/7916143/working/building/REAL250005061401 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/523 `/scratch/stefan/7916143/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061401.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061401 none CC(C)CCC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 199, 201, 186, 121, 70, 121, 52, 70, 17, 49, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 200, 201, 201, 201, 201, 199, 199, 186, 186, 70, 70, 70, 52, 52, 52, 52, 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: 835 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061401 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061401 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061401/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061401 Building REAL250005061402 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061402' /scratch/stefan/7916143/working/building/REAL250005061402 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061402 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061402/0 /scratch/stefan/7916143/working/building/REAL250005061402 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/524 `/scratch/stefan/7916143/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CC=CN1) `REAL250005061402.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061402 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [40, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 42, 73, 73, 123, 123, 165, 165, 165, 165, 42, 42, 42, 42, 12, 12, 4, 1, 73, 73, 73, 165, 165, 165, 165] 165 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 506 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061402 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [61, 24, 61, 122, 165, 165, 165, 165, 165, 165, 165, 165, 11, 24, 1, 11, 1, 1, 1, 1, 1, 61, 61, 61, 61, 122, 122, 165, 165, 24, 24, 24, 1, 1, 1, 1] 165 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 656 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061402 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061402 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061402/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061402 Building REAL250005061403 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061403' /scratch/stefan/7916143/working/building/REAL250005061403 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061403 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061403/0 /scratch/stefan/7916143/working/building/REAL250005061403 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/525 `/scratch/stefan/7916143/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=COC=C1) `REAL250005061403.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061403 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=COC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [44, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 47, 79, 79, 132, 132, 201, 201, 201, 201, 47, 47, 47, 47, 15, 15, 4, 1, 79, 79, 79, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 603 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061403 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=COC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [68, 28, 68, 144, 201, 201, 201, 201, 201, 201, 201, 201, 11, 28, 1, 11, 1, 1, 1, 1, 1, 68, 68, 68, 68, 144, 144, 201, 201, 28, 28, 28, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 818 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061403 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061403 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061403/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061403 Building REAL250005061404 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061404' /scratch/stefan/7916143/working/building/REAL250005061404 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061404 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061404/0 /scratch/stefan/7916143/working/building/REAL250005061404 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/526 `/scratch/stefan/7916143/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061404.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061404 none CCCCCC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 170, 162, 106, 57, 106, 44, 57, 15, 41, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 196, 196, 170, 170, 162, 162, 57, 57, 57, 44, 44, 44, 44, 15, 15, 4, 1] 201 rigid atoms, others: [42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 843 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061404 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061404 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061404/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061404 Building REAL250005061405 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061405' /scratch/stefan/7916143/working/building/REAL250005061405 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061405 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061405/0 /scratch/stefan/7916143/working/building/REAL250005061405 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/527 `/scratch/stefan/7916143/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC(C)(C)C) `REAL250005061405.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061405 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 49, 81, 81, 131, 131, 150, 152, 152, 152, 49, 49, 49, 49, 18, 18, 4, 1, 81, 81, 81, 150, 150, 152, 152, 152, 152, 152, 152, 152, 152, 152] 152 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 585 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061405 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061405 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061405/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061405 Building REAL250005061406 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061406' /scratch/stefan/7916143/working/building/REAL250005061406 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061406 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061406/0 /scratch/stefan/7916143/working/building/REAL250005061406 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/528 `/scratch/stefan/7916143/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061406.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061406 none CCCCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 182, 119, 67, 119, 48, 67, 17, 45, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 189, 189, 182, 182, 67, 67, 67, 48, 48, 48, 48, 17, 17, 4, 1] 201 rigid atoms, others: [39, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 829 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061406 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061406 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061406/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061406 Building REAL250005061407 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061407' /scratch/stefan/7916143/working/building/REAL250005061407 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061407 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061407/0 /scratch/stefan/7916143/working/building/REAL250005061407 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/529 `/scratch/stefan/7916143/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061407.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061407 none CC(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 107, 135, 78, 107, 34, 74, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 135, 135, 107, 107, 107, 78, 78, 78, 78, 34, 34, 9, 1] 135 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: 521 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061407 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061407 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061407/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061407 Building REAL250005061408 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061408' /scratch/stefan/7916143/working/building/REAL250005061408 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061408 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061408/0 /scratch/stefan/7916143/working/building/REAL250005061408 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/530 `/scratch/stefan/7916143/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061408.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061408 none CCC(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 160, 189, 114, 160, 84, 114, 28, 80, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 189, 189, 189, 189, 114, 114, 114, 84, 84, 84, 84, 28, 28, 7, 1] 201 rigid atoms, others: [39, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 833 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061408 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061408 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061408/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061408 Building REAL250005061409 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061409' /scratch/stefan/7916143/working/building/REAL250005061409 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061409 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061409/0 /scratch/stefan/7916143/working/building/REAL250005061409 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/531 `/scratch/stefan/7916143/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061409.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061409 none CCC(CC)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [186, 173, 134, 173, 186, 80, 134, 57, 80, 19, 53, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 187, 187, 187, 187, 187, 173, 192, 192, 192, 192, 192, 80, 80, 80, 57, 57, 57, 57, 19, 19, 6, 1] 193 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: 918 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061409 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061409 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061409/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061409 Building REAL250005061410 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061410' /scratch/stefan/7916143/working/building/REAL250005061410 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061410 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061410/0 /scratch/stefan/7916143/working/building/REAL250005061410 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/532 `/scratch/stefan/7916143/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=NNC=C1) `REAL250005061410.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061410 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=NNC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 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: [34, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 51, 51, 70, 70, 83, 83, 83, 83, 35, 35, 35, 35, 12, 12, 4, 1, 51, 51, 51, 83, 83, 83] 83 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061410 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=NNC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 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: [47, 29, 47, 65, 83, 83, 83, 83, 83, 83, 83, 83, 12, 29, 1, 12, 1, 1, 1, 1, 1, 47, 47, 47, 47, 65, 65, 83, 83, 29, 29, 29, 1, 1, 1] 83 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 329 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061410 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061410/1 /scratch/stefan/7916143/working/building/REAL250005061410 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/533 `/scratch/stefan/7916143/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CC=NN1) `REAL250005061410.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061410 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CC=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [43, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 47, 82, 82, 125, 125, 179, 179, 179, 179, 47, 47, 47, 47, 16, 16, 4, 1, 82, 82, 82, 179, 179, 179] 179 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 557 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061410 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CC=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [60, 22, 60, 134, 179, 179, 179, 179, 179, 179, 179, 179, 10, 22, 1, 10, 1, 1, 1, 1, 1, 60, 60, 60, 60, 134, 134, 179, 179, 22, 22, 22, 1, 1, 1] 179 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 737 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061410 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061410 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061410/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061410/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061410 Building REAL250005061411 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061411' /scratch/stefan/7916143/working/building/REAL250005061411 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061411 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061411/0 /scratch/stefan/7916143/working/building/REAL250005061411 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/534 `/scratch/stefan/7916143/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061411.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061411 none CCOC(C)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 188, 156, 188, 89, 156, 65, 89, 22, 61, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 188, 188, 188, 188, 89, 89, 89, 65, 65, 65, 65, 22, 22, 5, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 763 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061411 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061411 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061411/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061411 Building REAL250005061412 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061412' /scratch/stefan/7916143/working/building/REAL250005061412 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061412 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061412/0 /scratch/stefan/7916143/working/building/REAL250005061412 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/535 `/scratch/stefan/7916143/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CNN=C1) `REAL250005061412.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061412 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CNN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 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: [51, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 54, 81, 81, 122, 122, 122, 122, 122, 122, 54, 54, 54, 54, 20, 20, 8, 1, 81, 81, 81, 122, 122, 122] 122 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 435 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061412 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CNN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 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: [44, 21, 44, 77, 107, 107, 107, 107, 107, 107, 107, 107, 11, 21, 1, 11, 1, 1, 1, 1, 1, 44, 44, 44, 44, 77, 77, 107, 107, 21, 21, 21, 1, 1, 1] 107 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 436 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061412 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061412 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061412/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061412 Building REAL250005061413 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061413' /scratch/stefan/7916143/working/building/REAL250005061413 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061413 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061413/0 /scratch/stefan/7916143/working/building/REAL250005061413 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/536 `/scratch/stefan/7916143/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061413.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061413 none COCCCC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 140, 131, 90, 46, 90, 36, 46, 15, 36, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 198, 149, 149, 131, 131, 46, 46, 46, 36, 36, 36, 36, 15, 15, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 896 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061413 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061413 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061413/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061413 Building REAL250005061414 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061414' /scratch/stefan/7916143/working/building/REAL250005061414 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061414 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061414/0 /scratch/stefan/7916143/working/building/REAL250005061414 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/537 `/scratch/stefan/7916143/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=NOC=C1) `REAL250005061414.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061414 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=NOC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 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: [31, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 32, 47, 47, 61, 61, 68, 68, 68, 68, 32, 32, 32, 32, 14, 14, 4, 1, 47, 47, 47, 68, 68] 68 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061414 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=NOC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 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: [40, 24, 40, 55, 68, 68, 68, 68, 68, 68, 68, 68, 11, 24, 1, 11, 1, 1, 1, 1, 1, 40, 40, 40, 40, 55, 55, 68, 68, 24, 24, 24, 1, 1] 68 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061414 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061414 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061414/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061414 Building REAL250005061415 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061415' /scratch/stefan/7916143/working/building/REAL250005061415 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061415 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061415/0 /scratch/stefan/7916143/working/building/REAL250005061415 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/538 `/scratch/stefan/7916143/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061415.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061415 none CCC=C(C)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 187, 127, 187, 61, 127, 50, 61, 16, 48, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 187, 187, 187, 187, 61, 61, 61, 50, 50, 50, 50, 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: 745 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061415 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061415 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061415/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061415 Building REAL250005061416 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061416' /scratch/stefan/7916143/working/building/REAL250005061416 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061416 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061416/0 /scratch/stefan/7916143/working/building/REAL250005061416 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/539 `/scratch/stefan/7916143/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061416.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061416 none COC(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 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, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [98, 96, 88, 96, 64, 88, 53, 64, 24, 52, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 98, 98, 98, 96, 96, 96, 96, 64, 64, 64, 53, 53, 53, 53, 24, 24, 7, 1] 98 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: 376 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061416 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061416 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061416/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061416 Building REAL250005061417 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061417' /scratch/stefan/7916143/working/building/REAL250005061417 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061417 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061417/0 /scratch/stefan/7916143/working/building/REAL250005061417 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/540 `/scratch/stefan/7916143/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061417.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061417 none CC(C)OCC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 174, 201, 124, 93, 52, 93, 45, 52, 18, 45, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 124, 124, 52, 52, 52, 45, 45, 45, 45, 18, 18, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061417 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061417 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061417/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061417 Building REAL250005061418 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061418' /scratch/stefan/7916143/working/building/REAL250005061418 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061418 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061418/0 /scratch/stefan/7916143/working/building/REAL250005061418 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/541 `/scratch/stefan/7916143/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061418.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061418 none CCCOCC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 149, 89, 60, 39, 60, 34, 39, 13, 34, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 194, 194, 89, 89, 39, 39, 39, 34, 34, 34, 34, 13, 13, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 756 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061418 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061418 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061418/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061418 Building REAL250005061419 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061419' /scratch/stefan/7916143/working/building/REAL250005061419 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061419 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061419/0 /scratch/stefan/7916143/working/building/REAL250005061419 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/542 `/scratch/stefan/7916143/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCOC1) `REAL250005061419.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061419 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 12, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 68, 106, 106, 177, 177, 201, 201, 201, 201, 68, 68, 68, 68, 22, 22, 4, 1, 106, 106, 106, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 722 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061419 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 12, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 21, 58, 136, 201, 201, 201, 201, 201, 201, 201, 201, 6, 21, 1, 6, 1, 1, 1, 1, 1, 58, 58, 58, 58, 136, 136, 201, 201, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 791 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061419 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061419 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061419/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061419 Building REAL250005061420 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061420' /scratch/stefan/7916143/working/building/REAL250005061420 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061420 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061420/0 /scratch/stefan/7916143/working/building/REAL250005061420 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/543 `/scratch/stefan/7916143/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061420.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061420 none CCC(OC)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [103, 95, 72, 95, 100, 46, 72, 39, 46, 21, 39, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 95, 100, 100, 100, 46, 46, 46, 39, 39, 39, 39, 21, 21, 6, 1] 107 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: 497 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061420 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061420 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061420/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061420 Building REAL250005061421 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061421' /scratch/stefan/7916143/working/building/REAL250005061421 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061421 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061421/0 /scratch/stefan/7916143/working/building/REAL250005061421 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/544 `/scratch/stefan/7916143/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061421.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061421 none COC(C)CC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 168, 197, 129, 80, 129, 55, 80, 20, 52, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 197, 197, 197, 197, 168, 168, 80, 80, 80, 55, 55, 55, 55, 20, 20, 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: 853 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061421 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061421 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061421/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061421 Building REAL250005061422 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061422' /scratch/stefan/7916143/working/building/REAL250005061422 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061422 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061422/0 /scratch/stefan/7916143/working/building/REAL250005061422 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/545 `/scratch/stefan/7916143/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061422.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061422 none C=CCCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 4, 7, 6, 7, 7, 7, 3, 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, 200, 188, 147, 89, 147, 69, 89, 21, 65, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 188, 188, 89, 89, 89, 69, 69, 69, 69, 21, 21, 4, 1] 200 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: 798 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061422 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061422 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061422/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061422 Building REAL250005061423 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061423' /scratch/stefan/7916143/working/building/REAL250005061423 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061423 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061423/0 /scratch/stefan/7916143/working/building/REAL250005061423 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/546 `/scratch/stefan/7916143/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061423.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061423 none CCOCCC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 175, 169, 138, 79, 138, 61, 79, 19, 58, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 175, 175, 169, 169, 79, 79, 79, 61, 61, 61, 61, 19, 19, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 737 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061423 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061423 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061423/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061423 Building REAL250005061424 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061424' /scratch/stefan/7916143/working/building/REAL250005061424 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061424 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061424/0 /scratch/stefan/7916143/working/building/REAL250005061424 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/547 `/scratch/stefan/7916143/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061424.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061424 none COCC(C)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 185, 138, 185, 85, 138, 64, 85, 20, 62, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 185, 185, 185, 185, 85, 85, 85, 64, 64, 64, 64, 20, 20, 4, 1] 194 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 798 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061424 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061424 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061424/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061424 Building REAL250005061425 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061425' /scratch/stefan/7916143/working/building/REAL250005061425 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061425 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061425/0 /scratch/stefan/7916143/working/building/REAL250005061425 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/548 `/scratch/stefan/7916143/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061425.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061425 none C=CCOCC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 130, 82, 52, 33, 52, 28, 33, 12, 28, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 82, 82, 33, 33, 33, 28, 28, 28, 28, 12, 12, 4, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 822 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061425 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061425 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061425/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061425 Building REAL250005061426 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061426' /scratch/stefan/7916143/working/building/REAL250005061426 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061426 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061426/0 /scratch/stefan/7916143/working/building/REAL250005061426 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/549 `/scratch/stefan/7916143/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=COC=N1) `REAL250005061426.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061426 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=COC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [44, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 74, 74, 106, 106, 127, 127, 127, 127, 45, 45, 45, 45, 14, 14, 4, 1, 74, 74, 74, 127, 127] 127 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 420 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061426 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=COC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [59, 32, 59, 96, 127, 127, 127, 127, 127, 127, 127, 127, 12, 32, 1, 12, 1, 1, 1, 1, 1, 59, 59, 59, 59, 96, 96, 127, 127, 32, 32, 32, 1, 1] 127 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 514 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061426 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061426 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061426/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061426 Building REAL250005061427 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061427' /scratch/stefan/7916143/working/building/REAL250005061427 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061427 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061427/0 /scratch/stefan/7916143/working/building/REAL250005061427 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/550 `/scratch/stefan/7916143/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061427.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061427 none CCCC(C)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 193, 147, 193, 92, 147, 63, 92, 19, 59, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 200, 201, 201, 193, 193, 193, 193, 92, 92, 92, 63, 63, 63, 63, 19, 19, 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: 849 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061427 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061427 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061427/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061427 Building REAL250005061428 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061428' /scratch/stefan/7916143/working/building/REAL250005061428 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061428 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061428/0 /scratch/stefan/7916143/working/building/REAL250005061428 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/551 `/scratch/stefan/7916143/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CCC1CC1) `REAL250005061428.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061428 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 73, 73, 106, 106, 133, 142, 201, 201, 41, 41, 41, 41, 16, 16, 4, 1, 73, 73, 73, 133, 133, 142, 142, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 808 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061428 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 42, 72, 134, 201, 201, 201, 201, 201, 201, 201, 201, 24, 42, 7, 24, 3, 1, 1, 1, 1, 72, 72, 72, 72, 134, 134, 201, 201, 42, 42, 42, 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: 767 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061428 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061428 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061428/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061428 Building REAL250005061429 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061429' /scratch/stefan/7916143/working/building/REAL250005061429 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061429 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061429/0 /scratch/stefan/7916143/working/building/REAL250005061429 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/552 `/scratch/stefan/7916143/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC=CC1) `REAL250005061429.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061429 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 1, 1, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 66, 101, 101, 164, 164, 201, 201, 201, 201, 66, 66, 66, 66, 24, 24, 4, 1, 101, 101, 101, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 731 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061429 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 1, 1, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 62, 136, 201, 201, 201, 201, 201, 201, 201, 201, 6, 23, 1, 6, 1, 1, 1, 1, 1, 62, 62, 62, 62, 136, 136, 201, 201, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 780 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061429 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061429 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061429/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061429 Building REAL250005061430 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061430' /scratch/stefan/7916143/working/building/REAL250005061430 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061430 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061430/0 /scratch/stefan/7916143/working/building/REAL250005061430 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/553 `/scratch/stefan/7916143/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC1CCC1) `REAL250005061430.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061430 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 84, 84, 124, 124, 142, 201, 201, 201, 50, 50, 50, 50, 17, 17, 4, 1, 84, 84, 84, 142, 142, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 785 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061430 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 51, 82, 144, 201, 201, 201, 201, 201, 201, 201, 201, 26, 51, 7, 26, 1, 1, 1, 1, 1, 82, 82, 82, 82, 144, 144, 201, 201, 51, 51, 51, 7, 7, 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: 759 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061430 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061430 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061430/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061430 Building REAL250005061431 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061431' /scratch/stefan/7916143/working/building/REAL250005061431 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061431 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061431/0 /scratch/stefan/7916143/working/building/REAL250005061431 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/554 `/scratch/stefan/7916143/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(C)C1CC1) `REAL250005061431.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061431 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 46, 64, 63, 91, 91, 98, 98, 99, 99, 46, 46, 46, 46, 18, 18, 4, 1, 64, 64, 64, 98, 98, 98, 98, 99, 99, 99, 99, 99] 99 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 397 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061431 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 20, 37, 70, 99, 99, 99, 99, 99, 99, 99, 99, 9, 20, 4, 9, 1, 4, 1, 1, 1, 37, 37, 37, 37, 70, 70, 99, 99, 20, 20, 20, 4, 4, 4, 4, 1, 1, 1, 1, 1] 99 rigid atoms, others: [36, 37, 38, 39, 40, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 393 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061431 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061431 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061431/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061431 Building REAL250005061432 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061432' /scratch/stefan/7916143/working/building/REAL250005061432 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061432 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061432/0 /scratch/stefan/7916143/working/building/REAL250005061432 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/555 `/scratch/stefan/7916143/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061432.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061432 none CC=C(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 94, 136, 69, 94, 59, 69, 32, 59, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 136, 136, 136, 69, 69, 69, 59, 59, 59, 59, 32, 32, 9, 1] 136 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: 523 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061432 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061432 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061432/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061432 Building REAL250005061433 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061433' /scratch/stefan/7916143/working/building/REAL250005061433 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061433 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061433/0 /scratch/stefan/7916143/working/building/REAL250005061433 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/556 `/scratch/stefan/7916143/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC(C)C1) `REAL250005061433.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061433 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 56, 90, 90, 159, 159, 201, 201, 201, 201, 56, 56, 56, 56, 22, 22, 6, 1, 90, 90, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 716 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061433 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 58, 137, 200, 200, 200, 201, 201, 201, 201, 201, 8, 24, 1, 8, 1, 1, 1, 1, 1, 58, 58, 58, 58, 137, 137, 200, 201, 24, 24, 24, 1, 1, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 39, 40, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 792 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061433 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061433 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061433/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061433 Building REAL250005061434 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061434' /scratch/stefan/7916143/working/building/REAL250005061434 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061434 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061434/0 /scratch/stefan/7916143/working/building/REAL250005061434 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/557 `/scratch/stefan/7916143/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C=C1CCC1) `REAL250005061434.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061434 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C=C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 53, 91, 91, 158, 158, 201, 201, 201, 201, 53, 53, 53, 53, 20, 20, 4, 1, 91, 91, 91, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 710 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061434 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C=C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 73, 150, 201, 201, 201, 201, 201, 201, 201, 201, 9, 33, 1, 9, 1, 1, 1, 1, 1, 73, 73, 73, 73, 150, 150, 201, 201, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 816 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061434 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061434 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061434/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061434 Building REAL250005061435 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061435' /scratch/stefan/7916143/working/building/REAL250005061435 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061435 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061435/0 /scratch/stefan/7916143/working/building/REAL250005061435 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/558 `/scratch/stefan/7916143/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061435.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061435 none CC(C)=C(F)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 5, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 109, 129, 75, 109, 55, 75, 26, 55, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 129, 129, 75, 75, 75, 55, 55, 55, 55, 26, 26, 10, 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: 472 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061435 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061435 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061435/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061435 Building REAL250005061436 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061436' /scratch/stefan/7916143/working/building/REAL250005061436 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061436 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061436/0 /scratch/stefan/7916143/working/building/REAL250005061436 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/559 `/scratch/stefan/7916143/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CCCC1) `REAL250005061436.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061436 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [67, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 70, 104, 104, 153, 153, 153, 153, 153, 153, 70, 70, 70, 70, 24, 24, 4, 1, 104, 104, 104, 153, 153, 153, 153, 153, 153, 153] 153 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 561 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061436 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [58, 23, 58, 121, 153, 153, 153, 153, 153, 153, 153, 153, 8, 23, 1, 8, 1, 1, 1, 1, 1, 58, 58, 58, 58, 121, 121, 153, 153, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1] 153 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 624 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061436 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061436 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061436/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061436 Building REAL250005061437 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061437' /scratch/stefan/7916143/working/building/REAL250005061437 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061437 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061437/0 /scratch/stefan/7916143/working/building/REAL250005061437 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/560 `/scratch/stefan/7916143/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC1(C)C) `REAL250005061437.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061437 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 78, 120, 120, 186, 186, 201, 201, 201, 201, 78, 78, 78, 78, 28, 28, 6, 1, 120, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 721 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061437 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 21, 51, 133, 201, 201, 201, 201, 201, 201, 201, 201, 6, 21, 1, 6, 1, 1, 1, 1, 1, 51, 51, 51, 51, 133, 133, 201, 201, 21, 21, 21, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 778 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061437 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061437 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061437/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061437 Building REAL250005061438 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061438' /scratch/stefan/7916143/working/building/REAL250005061438 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061438 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061438/0 /scratch/stefan/7916143/working/building/REAL250005061438 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/561 `/scratch/stefan/7916143/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H]1CC1(C)C) `REAL250005061438.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061438 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H]1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [69, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 72, 111, 111, 175, 175, 191, 191, 191, 191, 191, 72, 72, 72, 72, 27, 27, 8, 1, 111, 111, 111, 191, 191, 191, 191, 191, 191, 191, 191] 191 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 671 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061438 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H]1CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [53, 23, 53, 129, 190, 190, 190, 191, 191, 191, 191, 191, 6, 23, 1, 6, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 129, 129, 190, 191, 23, 23, 23, 1, 1, 2, 2, 2, 2, 2, 2] 191 rigid atoms, others: [33, 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, 35, 36, 37, 38, 39, 40]) total number of confs: 741 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061438 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061438 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061438/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061438 Building REAL250005061439 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061439' /scratch/stefan/7916143/working/building/REAL250005061439 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061439 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061439/0 /scratch/stefan/7916143/working/building/REAL250005061439 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/562 `/scratch/stefan/7916143/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H]1CCCO1) `REAL250005061439.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061439 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [43, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 44, 57, 57, 76, 76, 88, 88, 88, 88, 88, 44, 44, 44, 44, 18, 18, 4, 1, 57, 57, 57, 88, 88, 88, 88, 88, 88] 88 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 336 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061439 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [40, 21, 40, 68, 88, 88, 88, 88, 88, 88, 88, 88, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 68, 68, 88, 88, 21, 21, 21, 1, 1, 1, 1, 1, 1] 88 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 356 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061439 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061439 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061439/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061439 Building REAL250005061440 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061440' /scratch/stefan/7916143/working/building/REAL250005061440 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061440 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061440/0 /scratch/stefan/7916143/working/building/REAL250005061440 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/563 `/scratch/stefan/7916143/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061440.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061440 none CCC(C)CC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 161, 193, 97, 54, 97, 42, 54, 14, 41, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 193, 193, 193, 161, 161, 54, 54, 54, 42, 42, 42, 42, 14, 14, 4, 1] 201 rigid atoms, others: [42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 884 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061440 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061440 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061440/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061440 Building REAL250005061441 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061441' /scratch/stefan/7916143/working/building/REAL250005061441 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061441 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061441/0 /scratch/stefan/7916143/working/building/REAL250005061441 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/564 `/scratch/stefan/7916143/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061441.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061441 none C#CCCCC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 113, 71, 43, 71, 37, 43, 14, 36, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 197, 198, 131, 131, 113, 113, 43, 43, 43, 37, 37, 37, 37, 14, 14, 4, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 956 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061441 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061441 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061441/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061441 Building REAL250005061442 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061442' /scratch/stefan/7916143/working/building/REAL250005061442 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061442 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061442/0 /scratch/stefan/7916143/working/building/REAL250005061442 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/565 `/scratch/stefan/7916143/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC(C)(C)O) `REAL250005061442.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061442 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 7, 7] 1 hydrogens need rotated 429 conformations in input total number of sets (complete confs): 429 using faster count positions algorithm for large data unique positions, atoms: [43, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 46, 72, 72, 119, 119, 138, 143, 143, 143, 46, 46, 46, 46, 17, 17, 4, 1, 72, 72, 72, 138, 138, 143, 143, 143, 143, 143, 143, 429] 429 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 993 number of broken/clashed sets: 189 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061442 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061442 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061442/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061442 Building REAL250005061443 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061443' /scratch/stefan/7916143/working/building/REAL250005061443 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061443 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061443/0 /scratch/stefan/7916143/working/building/REAL250005061443 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/566 `/scratch/stefan/7916143/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061443.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061443 none CC(C)[C@@H](O)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 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] 1 hydrogens need rotated 315 conformations in input total number of sets (complete confs): 315 using faster count positions algorithm for large data unique positions, atoms: [105, 92, 105, 71, 92, 92, 45, 71, 36, 45, 18, 36, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 105, 105, 276, 45, 45, 45, 36, 36, 36, 36, 18, 18, 5, 1] 315 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: 735 number of broken/clashed sets: 134 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061443 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061443 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061443/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061443 Building REAL250005061444 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061444' /scratch/stefan/7916143/working/building/REAL250005061444 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061444 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061444/0 /scratch/stefan/7916143/working/building/REAL250005061444 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/567 `/scratch/stefan/7916143/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061444.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061444 none CCC(C)=CC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 143, 143, 143, 106, 64, 106, 50, 64, 17, 49, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 143, 143, 143, 143, 64, 64, 64, 50, 50, 50, 50, 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: 872 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061444 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061444 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061444/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061444 Building REAL250005061445 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061445' /scratch/stefan/7916143/working/building/REAL250005061445 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061445 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061445/0 /scratch/stefan/7916143/working/building/REAL250005061445 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/568 `/scratch/stefan/7916143/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C#CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061445.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061445 none CC(C)C#CC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', '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, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 73, 89, 60, 73, 36, 59, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 89, 89, 73, 73, 73, 60, 60, 60, 60, 36, 36, 10, 1] 89 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: 345 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061445 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061445 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061445/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061445 Building REAL250005061446 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061446' /scratch/stefan/7916143/working/building/REAL250005061446 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061446 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061446/0 /scratch/stefan/7916143/working/building/REAL250005061446 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/569 `/scratch/stefan/7916143/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C#CC1CC1) `REAL250005061446.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061446 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C#CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [66, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 69, 95, 95, 136, 136, 136, 136, 136, 136, 69, 69, 69, 69, 30, 30, 8, 1, 95, 95, 95, 136, 136, 136, 136, 136] 136 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 493 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061446 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C#CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [25, 6, 25, 79, 128, 128, 128, 136, 136, 136, 136, 136, 1, 6, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 79, 79, 128, 136, 7, 7, 7, 1, 1, 1, 1, 1] 136 rigid atoms, others: [32, 33, 34, 35, 36, 12, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 503 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061446 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061446 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061446/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061446 Building REAL250005061447 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061447' /scratch/stefan/7916143/working/building/REAL250005061447 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061447 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061447/0 /scratch/stefan/7916143/working/building/REAL250005061447 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/570 `/scratch/stefan/7916143/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061447.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061447 none C=C(C)CCC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 183, 183, 181, 131, 78, 131, 61, 78, 17, 57, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 183, 183, 183, 183, 183, 183, 183, 181, 181, 78, 78, 78, 61, 61, 61, 61, 17, 17, 5, 1] 183 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: 743 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061447 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061447 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061447/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061447 Building REAL250005061448 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061448' /scratch/stefan/7916143/working/building/REAL250005061448 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061448 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061448/0 /scratch/stefan/7916143/working/building/REAL250005061448 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/571 `/scratch/stefan/7916143/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(C)CC1) `REAL250005061448.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061448 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [47, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 50, 70, 70, 87, 87, 87, 87, 87, 50, 50, 50, 50, 26, 26, 9, 1, 70, 70, 70, 87, 87, 87, 87, 87, 87, 87] 87 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 328 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061448 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 50, 80, 80, 80, 87, 87, 87, 87, 87, 3, 7, 1, 3, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 80, 87, 7, 7, 7, 2, 2, 2, 1, 1, 1, 1] 87 rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 321 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061448 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061448 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061448/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061448 Building REAL250005061449 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061449' /scratch/stefan/7916143/working/building/REAL250005061449 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061449 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061449/0 /scratch/stefan/7916143/working/building/REAL250005061449 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/572 `/scratch/stefan/7916143/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H]1CCCO1) `REAL250005061449.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061449 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 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: [41, 15, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 42, 53, 53, 71, 71, 80, 80, 80, 80, 80, 42, 42, 42, 42, 15, 15, 3, 1, 53, 53, 53, 80, 80, 80, 80, 80, 80] 80 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 299 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061449 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 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: [39, 22, 39, 63, 80, 80, 80, 80, 80, 80, 80, 80, 6, 22, 1, 6, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 63, 63, 80, 80, 22, 22, 22, 1, 1, 1, 1, 1, 1] 80 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 323 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061449 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061449 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061449/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061449 Building REAL250005061450 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061450' /scratch/stefan/7916143/working/building/REAL250005061450 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061450 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061450/0 /scratch/stefan/7916143/working/building/REAL250005061450 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/573 `/scratch/stefan/7916143/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=NNN=C1) `REAL250005061450.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061450 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=NNN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 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: [29, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 30, 48, 48, 64, 64, 71, 71, 71, 71, 30, 30, 30, 30, 13, 13, 4, 1, 48, 48, 48, 71, 71] 71 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061450 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=NNN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 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: [40, 23, 40, 60, 71, 71, 71, 71, 71, 71, 71, 71, 12, 23, 1, 12, 1, 1, 1, 1, 1, 40, 40, 40, 40, 60, 60, 71, 71, 23, 23, 23, 1, 1] 71 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061450 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061450 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061450/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061450 Building REAL250005061451 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061451' /scratch/stefan/7916143/working/building/REAL250005061451 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061451 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061451/0 /scratch/stefan/7916143/working/building/REAL250005061451 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/574 `/scratch/stefan/7916143/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC1(C)CC1) `REAL250005061451.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061451 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 75, 75, 119, 119, 177, 201, 201, 201, 50, 50, 50, 50, 16, 16, 4, 1, 75, 75, 75, 177, 177, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 805 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061451 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 81, 133, 201, 201, 201, 201, 201, 201, 201, 201, 20, 48, 8, 20, 1, 1, 1, 1, 1, 81, 81, 81, 81, 133, 133, 201, 201, 48, 48, 48, 8, 8, 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: 770 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061451 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061451 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061451/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061451 Building REAL250005061452 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061452' /scratch/stefan/7916143/working/building/REAL250005061452 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061452 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061452/0 /scratch/stefan/7916143/working/building/REAL250005061452 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/575 `/scratch/stefan/7916143/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CN=CO1) `REAL250005061452.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061452 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CN=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [61, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 63, 101, 101, 156, 156, 189, 189, 189, 189, 63, 63, 63, 63, 22, 22, 4, 1, 101, 101, 101, 189, 189] 189 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 587 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061452 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CN=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [79, 35, 79, 146, 189, 189, 189, 189, 189, 189, 189, 189, 12, 35, 1, 12, 1, 1, 1, 1, 1, 79, 79, 79, 79, 146, 146, 189, 189, 35, 35, 35, 1, 1] 189 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 759 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061452 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061452 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061452/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061452 Building REAL250005061453 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061453' /scratch/stefan/7916143/working/building/REAL250005061453 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061453 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061453/0 /scratch/stefan/7916143/working/building/REAL250005061453 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/576 `/scratch/stefan/7916143/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061453.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061453 none C=CC(C)(C)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 17, 18, 15, 17, 10, 15, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 17, 17, 17, 15, 15, 15, 15, 10, 10, 4, 1] 18 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: 76 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061453 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061453 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061453/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061453 Building REAL250005061454 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061454' /scratch/stefan/7916143/working/building/REAL250005061454 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061454 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061454/0 /scratch/stefan/7916143/working/building/REAL250005061454 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/577 `/scratch/stefan/7916143/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H]1C[C@H]1C) `REAL250005061454.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061454 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 71, 111, 111, 158, 158, 201, 201, 201, 201, 201, 71, 71, 71, 71, 25, 25, 5, 1, 111, 111, 111, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 741 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061454 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 64, 138, 200, 200, 200, 201, 201, 201, 201, 201, 8, 26, 1, 8, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 138, 138, 200, 201, 26, 26, 26, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 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, 35, 36, 37]) total number of confs: 792 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061454 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061454 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061454/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061454 Building REAL250005061455 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061455' /scratch/stefan/7916143/working/building/REAL250005061455 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061455 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061455/0 /scratch/stefan/7916143/working/building/REAL250005061455 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/578 `/scratch/stefan/7916143/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(C)CCC1) `REAL250005061455.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061455 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 46, 61, 61, 79, 79, 79, 79, 79, 79, 46, 46, 46, 46, 26, 26, 9, 1, 61, 61, 61, 79, 79, 79, 79, 79, 79, 79, 79, 79] 79 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061455 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(C)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 4, 13, 44, 67, 67, 67, 79, 79, 79, 79, 79, 3, 4, 1, 3, 1, 1, 1, 1, 1, 13, 13, 13, 13, 44, 44, 67, 79, 4, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1] 79 rigid atoms, others: [35, 36, 37, 38, 39, 40, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061455 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061455 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061455/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061455 Building REAL250005061456 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061456' /scratch/stefan/7916143/working/building/REAL250005061456 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061456 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061456/0 /scratch/stefan/7916143/working/building/REAL250005061456 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/579 `/scratch/stefan/7916143/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061456.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061456 none CCC(F)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 81, 61, 81, 44, 61, 32, 44, 19, 32, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 81, 44, 44, 44, 32, 32, 32, 32, 19, 19, 6, 1] 90 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: 371 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061456 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061456 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061456/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061456 Building REAL250005061457 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061457' /scratch/stefan/7916143/working/building/REAL250005061457 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061457 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061457/0 /scratch/stefan/7916143/working/building/REAL250005061457 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/580 `/scratch/stefan/7916143/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CCCF) `REAL250005061457.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061457 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CCCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 44, 80, 80, 140, 140, 176, 201, 201, 44, 44, 44, 44, 14, 14, 4, 1, 80, 80, 80, 176, 176, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 820 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061457 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061457 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061457/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061457 Building REAL250005061458 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061458' /scratch/stefan/7916143/working/building/REAL250005061458 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061458 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061458/0 /scratch/stefan/7916143/working/building/REAL250005061458 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/581 `/scratch/stefan/7916143/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H]1C[C@@H]1C) `REAL250005061458.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061458 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H]1C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 24, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 72, 111, 111, 165, 165, 201, 201, 201, 201, 201, 72, 72, 72, 72, 24, 24, 5, 1, 111, 111, 111, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 741 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061458 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H]1C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 72, 144, 200, 200, 200, 201, 201, 201, 201, 201, 8, 27, 1, 8, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 144, 144, 200, 201, 27, 27, 27, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 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, 35, 36, 37]) total number of confs: 790 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061458 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061458 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061458/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061458 Building REAL250005061459 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061459' /scratch/stefan/7916143/working/building/REAL250005061459 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061459 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061459/0 /scratch/stefan/7916143/working/building/REAL250005061459 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/582 `/scratch/stefan/7916143/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061459.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061459 none C=CCCCC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 131, 119, 86, 45, 86, 39, 45, 15, 39, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 198, 135, 135, 119, 119, 45, 45, 45, 39, 39, 39, 39, 15, 15, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 890 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061459 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061459 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061459/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061459 Building REAL250005061460 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061460' /scratch/stefan/7916143/working/building/REAL250005061460 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061460 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061460/0 /scratch/stefan/7916143/working/building/REAL250005061460 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/583 `/scratch/stefan/7916143/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061460.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061460 none CCC(C)(C)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 87, 49, 87, 87, 41, 49, 30, 41, 13, 30, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 87, 87, 87, 87, 87, 87, 41, 41, 41, 30, 30, 30, 30, 13, 13, 4, 1] 103 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: 486 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061460 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061460 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061460/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061460 Building REAL250005061461 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061461' /scratch/stefan/7916143/working/building/REAL250005061461 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061461 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061461/0 /scratch/stefan/7916143/working/building/REAL250005061461 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/584 `/scratch/stefan/7916143/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(N)=O) `REAL250005061461.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061461 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 19, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 45, 60, 60, 72, 72, 77, 77, 45, 45, 45, 45, 19, 19, 6, 1, 60, 60, 60, 77, 77] 77 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 26] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 295 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061461 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061461 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061461/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061461 Building REAL250005061462 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061462' /scratch/stefan/7916143/working/building/REAL250005061462 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061462 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061462/0 /scratch/stefan/7916143/working/building/REAL250005061462 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/585 `/scratch/stefan/7916143/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC1CC1C) `REAL250005061462.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061462 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC1CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 72, 72, 110, 110, 146, 201, 201, 201, 45, 45, 45, 45, 17, 17, 4, 1, 72, 72, 72, 146, 146, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 814 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061462 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC1CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 81, 145, 201, 201, 201, 201, 201, 201, 201, 201, 28, 48, 6, 28, 1, 1, 1, 1, 1, 81, 81, 81, 81, 145, 145, 201, 201, 48, 48, 48, 6, 6, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 37, 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, 38, 39, 40]) total number of confs: 817 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061462 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061462 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061462/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061462 Building REAL250005061463 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061463' /scratch/stefan/7916143/working/building/REAL250005061463 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061463 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061463/0 /scratch/stefan/7916143/working/building/REAL250005061463 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/586 `/scratch/stefan/7916143/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)N(C)C(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005061463.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061463 none CCC1(C(=O)N(C)C(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 3, 3, 7, 7, 15, 15, 43, 69, 69, 69, 70, 70, 70, 70, 70, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 15, 15, 15, 15, 43, 43, 69, 70, 1, 1, 1, 1] 70 rigid atoms, others: [1, 2, 3, 37, 38, 39, 40, 19, 20] 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, 35, 36]) total number of confs: 281 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061463 none CCC1(C(=O)N(C)C(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 49, 70, 36, 49, 17, 36, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 49, 49, 49, 36, 36, 36, 36, 17, 17, 4, 1, 70, 70, 70, 70] 70 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: 247 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061463 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061463 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061463/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061463 Building REAL250005061464 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061464' /scratch/stefan/7916143/working/building/REAL250005061464 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061464 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061464/0 /scratch/stefan/7916143/working/building/REAL250005061464 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/587 `/scratch/stefan/7916143/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(CF)CC1) `REAL250005061464.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061464 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(CF)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 15, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 71, 117, 117, 173, 173, 193, 201, 193, 193, 71, 71, 71, 71, 21, 21, 4, 1, 117, 117, 117, 201, 201, 193, 193, 193, 193] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 755 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061464 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(CF)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 15, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 81, 182, 182, 182, 193, 193, 193, 193, 193, 3, 9, 1, 3, 1, 1, 10, 1, 1, 27, 27, 27, 27, 81, 81, 182, 193, 9, 9, 9, 10, 10, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 14, 16, 17, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 668 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061464 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061464 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061464/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061464 Building REAL250005061465 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061465' /scratch/stefan/7916143/working/building/REAL250005061465 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061465 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061465/0 /scratch/stefan/7916143/working/building/REAL250005061465 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/588 `/scratch/stefan/7916143/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(C)(C)C) `REAL250005061465.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061465 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 20, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 33, 46, 46, 46, 46, 46, 46, 46, 33, 33, 33, 33, 20, 20, 8, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 46 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 185 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061465 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061465 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061465/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061465 Building REAL250005061466 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061466' /scratch/stefan/7916143/working/building/REAL250005061466 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061466 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061466/0 /scratch/stefan/7916143/working/building/REAL250005061466 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/589 `/scratch/stefan/7916143/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061466.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061466 none CC(C)C(C)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 148, 161, 125, 148, 82, 125, 61, 82, 21, 58, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 161, 161, 161, 148, 148, 148, 148, 82, 82, 82, 61, 61, 61, 61, 21, 21, 6, 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: 652 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061466 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061466 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061466/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061466 Building REAL250005061467 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061467' /scratch/stefan/7916143/working/building/REAL250005061467 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061467 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061467/0 /scratch/stefan/7916143/working/building/REAL250005061467 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/590 `/scratch/stefan/7916143/working/3D/590' -> `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)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061467.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061467 none CC[C@@H]1C[C@H]1C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 27, 38, 38, 96, 181, 181, 181, 192, 192, 192, 192, 192, 3, 3, 3, 3, 3, 1, 1, 27, 27, 27, 38, 38, 38, 38, 96, 96, 181, 192] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 660 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061467 none CC[C@@H]1C[C@H]1C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 192, 192, 192, 138, 192, 78, 138, 58, 78, 19, 56, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 192, 192, 78, 78, 78, 58, 58, 58, 58, 18, 18, 5, 1] 201 rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 728 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061467 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061467 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061467/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061467 Building REAL250005061468 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061468' /scratch/stefan/7916143/working/building/REAL250005061468 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061468 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061468/0 /scratch/stefan/7916143/working/building/REAL250005061468 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/591 `/scratch/stefan/7916143/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC12CC2) `REAL250005061468.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061468 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC12CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 58, 98, 98, 168, 168, 201, 201, 201, 201, 58, 58, 58, 58, 19, 19, 4, 1, 98, 98, 98, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 712 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061468 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC12CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 65, 141, 201, 201, 201, 201, 201, 201, 201, 201, 8, 27, 1, 8, 1, 1, 1, 1, 1, 65, 65, 65, 65, 141, 141, 201, 201, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 799 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061468 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061468 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061468/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061468 Building REAL250005061469 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061469' /scratch/stefan/7916143/working/building/REAL250005061469 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061469 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061469/0 /scratch/stefan/7916143/working/building/REAL250005061469 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/592 `/scratch/stefan/7916143/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H]1CC(=O)N1) `REAL250005061469.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061469 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H]1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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: [55, 22, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 57, 83, 83, 99, 99, 114, 114, 114, 114, 114, 57, 57, 57, 57, 21, 21, 5, 1, 83, 83, 83, 114, 114, 114] 114 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 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: 429 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061469 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H]1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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: [47, 24, 47, 84, 113, 113, 113, 114, 114, 114, 114, 114, 7, 24, 1, 7, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 84, 84, 113, 114, 24, 24, 24, 1, 1, 1] 114 rigid atoms, others: [33, 34, 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]) total number of confs: 443 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061469 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061469 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061469/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061469 Building REAL250005061470 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061470' /scratch/stefan/7916143/working/building/REAL250005061470 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061470 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061470/0 /scratch/stefan/7916143/working/building/REAL250005061470 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/593 `/scratch/stefan/7916143/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H]1CC(=O)N1) `REAL250005061470.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061470 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H]1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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: [56, 21, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 59, 84, 83, 107, 107, 127, 127, 127, 127, 127, 59, 59, 59, 59, 20, 20, 4, 1, 84, 84, 84, 127, 127, 127] 127 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 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: 489 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061470 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H]1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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: [56, 26, 56, 95, 127, 127, 127, 127, 127, 127, 127, 127, 7, 26, 1, 7, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 95, 95, 127, 127, 26, 26, 26, 1, 1, 1] 127 rigid atoms, others: [33, 34, 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]) total number of confs: 513 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061470 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061470 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061470/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061470 Building REAL250005061471 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061471' /scratch/stefan/7916143/working/building/REAL250005061471 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061471 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061471/0 /scratch/stefan/7916143/working/building/REAL250005061471 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/594 `/scratch/stefan/7916143/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)N(C)C(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005061471.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061471 none COC1(C(=O)N(C)C(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 5, 5, 16, 16, 23, 23, 64, 102, 102, 102, 102, 102, 102, 102, 102, 1, 1, 5, 5, 5, 16, 16, 16, 23, 23, 23, 23, 64, 64, 102, 102, 1, 1, 1, 1] 102 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: 383 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061471 none COC1(C(=O)N(C)C(C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 76, 60, 76, 53, 60, 21, 51, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 102, 60, 60, 60, 53, 53, 53, 53, 21, 21, 5, 1, 102, 102, 102, 102] 102 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: 402 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061471 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061471 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061471/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061471 Building REAL250005061472 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061472' /scratch/stefan/7916143/working/building/REAL250005061472 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061472 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061472/0 /scratch/stefan/7916143/working/building/REAL250005061472 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/595 `/scratch/stefan/7916143/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CSC1) `REAL250005061472.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061472 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CSC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 26, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 73, 115, 115, 173, 173, 201, 201, 201, 73, 73, 73, 73, 26, 26, 4, 1, 115, 115, 115, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 753 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061472 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CSC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 24, 63, 139, 201, 201, 201, 201, 201, 201, 201, 201, 7, 24, 1, 7, 1, 1, 1, 1, 63, 63, 63, 63, 139, 139, 201, 201, 24, 24, 24, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 791 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061472 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061472 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061472/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061472 Building REAL250005061473 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061473' /scratch/stefan/7916143/working/building/REAL250005061473 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061473 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061473/0 /scratch/stefan/7916143/working/building/REAL250005061473 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/596 `/scratch/stefan/7916143/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061473.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061473 none C=CCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 132, 89, 132, 69, 89, 27, 67, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 89, 89, 89, 69, 69, 69, 69, 27, 27, 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: 842 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061473 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061473 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061473/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061473 Building REAL250005061474 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061474' /scratch/stefan/7916143/working/building/REAL250005061474 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061474 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061474/0 /scratch/stefan/7916143/working/building/REAL250005061474 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/597 `/scratch/stefan/7916143/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C[NH+](C)C) `REAL250005061474.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061474 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 9, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 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: [10, 7, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 11, 11, 11, 11, 10, 10, 10, 10, 7, 7, 4, 1, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 47 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061474 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061474/1 /scratch/stefan/7916143/working/building/REAL250005061474 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/598 `/scratch/stefan/7916143/working/3D/598' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CN(C)C) `REAL250005061474.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061474/1/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: REAL250005061474 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 10, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [49, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 51, 83, 83, 117, 117, 180, 189, 189, 51, 51, 51, 51, 17, 17, 4, 1, 83, 83, 83, 180, 180, 189, 189, 189, 189, 189, 189] 189 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 782 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061474 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061474 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061474/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061474/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061474 Building REAL250005061475 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061475' /scratch/stefan/7916143/working/building/REAL250005061475 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061475 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061475/0 /scratch/stefan/7916143/working/building/REAL250005061475 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/599 `/scratch/stefan/7916143/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061475.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061475 none C=CC(O)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [116, 116, 85, 116, 53, 85, 44, 53, 22, 44, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 348, 53, 53, 53, 44, 44, 44, 44, 22, 22, 6, 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: 845 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061475 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061475 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061475/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061475 Building REAL250005061476 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061476' /scratch/stefan/7916143/working/building/REAL250005061476 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061476 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061476/0 /scratch/stefan/7916143/working/building/REAL250005061476 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/600 `/scratch/stefan/7916143/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1COC1) `REAL250005061476.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061476 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 22, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 77, 118, 118, 172, 172, 201, 201, 201, 77, 77, 77, 77, 22, 22, 5, 1, 118, 118, 118, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 750 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061476 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 24, 60, 142, 200, 200, 200, 201, 201, 201, 201, 201, 8, 24, 1, 8, 1, 1, 1, 1, 60, 60, 60, 60, 142, 142, 200, 201, 24, 24, 24, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 787 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061476 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061476 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061476/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061476 Building REAL250005061477 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061477' /scratch/stefan/7916143/working/building/REAL250005061477 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061477 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061477/0 /scratch/stefan/7916143/working/building/REAL250005061477 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/601 `/scratch/stefan/7916143/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061477.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061477 none CO[C@H](C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 95, 87, 95, 95, 64, 87, 53, 64, 24, 52, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 97, 97, 97, 95, 95, 95, 64, 64, 64, 53, 53, 53, 53, 24, 24, 7, 1] 97 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: 368 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061477 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061477 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061477/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061477 Building REAL250005061478 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061478' /scratch/stefan/7916143/working/building/REAL250005061478 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061478 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061478/0 /scratch/stefan/7916143/working/building/REAL250005061478 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/602 `/scratch/stefan/7916143/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(O)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061478.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061478 none CC=CC(O)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 441 conformations in input total number of sets (complete confs): 441 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 140, 112, 140, 66, 112, 50, 66, 17, 50, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 147, 140, 420, 66, 66, 66, 50, 50, 50, 50, 17, 17, 4, 1] 441 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: 1005 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061478 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061478 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061478/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061478 Building REAL250005061479 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061479' /scratch/stefan/7916143/working/building/REAL250005061479 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061479 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061479/0 /scratch/stefan/7916143/working/building/REAL250005061479 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/603 `/scratch/stefan/7916143/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H](C)[NH+](C)C) `REAL250005061479.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061479 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H](C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 9, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 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, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 8, 8, 4, 1, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 49 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061479 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061479/1 /scratch/stefan/7916143/working/building/REAL250005061479 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/604 `/scratch/stefan/7916143/working/3D/604' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H](C)N(C)C) `REAL250005061479.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061479/1/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: REAL250005061479 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H](C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 10, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 17, 20, 20, 26, 26, 27, 27, 27, 27, 27, 17, 17, 17, 17, 12, 12, 4, 1, 20, 20, 20, 27, 27, 27, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061479 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061479 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061479/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061479/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061479 Building REAL250005061480 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061480' /scratch/stefan/7916143/working/building/REAL250005061480 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061480 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061480/0 /scratch/stefan/7916143/working/building/REAL250005061480 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/605 `/scratch/stefan/7916143/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(F)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061480.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061480 none CCC=C(F)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 157, 157, 102, 157, 55, 102, 46, 55, 16, 45, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 157, 55, 55, 55, 46, 46, 46, 46, 16, 16, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 812 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061480 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061480 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061480/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061480 Building REAL250005061481 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061481' /scratch/stefan/7916143/working/building/REAL250005061481 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061481 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061481/0 /scratch/stefan/7916143/working/building/REAL250005061481 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/606 `/scratch/stefan/7916143/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061481.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061481 none CCC=CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 117, 67, 117, 55, 67, 20, 53, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 159, 159, 67, 67, 67, 55, 55, 55, 55, 20, 20, 4, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 817 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061481 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061481 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061481/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061481 Building REAL250005061482 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061482' /scratch/stefan/7916143/working/building/REAL250005061482 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005061482 as failed and skipping /scratch/stefan/7916143/working /scratch/stefan/7916143 `/scratch/stefan/7916143/working/building/REAL250005061482' -> `/scratch/stefan/7916143/failed/REAL250005061482' Building REAL250005061483 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061483' /scratch/stefan/7916143/working/building/REAL250005061483 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061483 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061483/0 /scratch/stefan/7916143/working/building/REAL250005061483 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/607 `/scratch/stefan/7916143/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(C)(C)CO) `REAL250005061483.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061483 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(C)(C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 7, 7] 1 hydrogens need rotated 492 conformations in input total number of sets (complete confs): 492 using faster count positions algorithm for large data unique positions, atoms: [61, 21, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 63, 91, 91, 96, 96, 164, 164, 164, 164, 63, 63, 63, 63, 21, 21, 4, 1, 91, 91, 91, 164, 164, 164, 164, 164, 164, 164, 164, 492] 492 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1200 number of broken/clashed sets: 492 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061483 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061483 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061483/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061483 Building REAL250005061484 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061484' /scratch/stefan/7916143/working/building/REAL250005061484 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061484 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061484/0 /scratch/stefan/7916143/working/building/REAL250005061484 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/608 `/scratch/stefan/7916143/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(F)CCC1) `REAL250005061484.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061484 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(F)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 15, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 32, 46, 46, 64, 64, 79, 79, 79, 79, 32, 32, 32, 32, 14, 14, 4, 1, 46, 46, 46, 79, 79, 79, 79, 79, 79] 79 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 293 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061484 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(F)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 15, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 18, 37, 60, 79, 79, 79, 79, 79, 79, 79, 79, 7, 18, 1, 7, 1, 1, 1, 1, 1, 37, 37, 37, 37, 60, 60, 79, 79, 18, 18, 18, 1, 1, 1, 1, 1, 1] 79 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 318 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061484 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061484 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061484/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061484 Building REAL250005061485 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061485' /scratch/stefan/7916143/working/building/REAL250005061485 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061485 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061485/0 /scratch/stefan/7916143/working/building/REAL250005061485 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/609 `/scratch/stefan/7916143/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CO) `REAL250005061485.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061485 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 288 conformations in input total number of sets (complete confs): 288 using faster count positions algorithm for large data unique positions, atoms: [56, 22, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 58, 80, 80, 88, 88, 96, 58, 58, 58, 58, 22, 22, 6, 1, 80, 80, 80, 96, 96, 288] 288 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 25] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 673 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061485 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061485 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061485/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061485 Building REAL250005061486 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061486' /scratch/stefan/7916143/working/building/REAL250005061486 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061486 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061486/0 /scratch/stefan/7916143/working/building/REAL250005061486 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/610 `/scratch/stefan/7916143/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C=CC(N)=O) `REAL250005061486.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061486 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C=CC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [26, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 27, 43, 43, 63, 63, 84, 84, 90, 90, 27, 27, 27, 27, 12, 12, 4, 1, 43, 43, 43, 84, 84, 90, 90] 90 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 342 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061486 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061486 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061486/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061486 Building REAL250005061487 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061487' /scratch/stefan/7916143/working/building/REAL250005061487 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061487 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061487/0 /scratch/stefan/7916143/working/building/REAL250005061487 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/611 `/scratch/stefan/7916143/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061487.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061487 none CC(O)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 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, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 207 conformations in input total number of sets (complete confs): 207 using faster count positions algorithm for large data unique positions, atoms: [69, 63, 69, 53, 63, 43, 53, 19, 43, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 207, 53, 53, 53, 43, 43, 43, 43, 19, 19, 6, 1] 207 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: 494 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061487 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061487 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061487/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061487 Building REAL250005061488 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061488' /scratch/stefan/7916143/working/building/REAL250005061488 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061488 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061488/0 /scratch/stefan/7916143/working/building/REAL250005061488 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/612 `/scratch/stefan/7916143/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(O)CCC1) `REAL250005061488.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061488 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 28, 38, 38, 47, 47, 57, 57, 57, 57, 28, 28, 28, 28, 13, 13, 4, 1, 38, 38, 38, 171, 57, 57, 57, 57, 57, 57] 171 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 393 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061488 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 16, 31, 48, 57, 57, 57, 57, 57, 57, 57, 57, 7, 16, 1, 7, 1, 1, 1, 1, 1, 31, 31, 31, 31, 48, 48, 57, 57, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1] 171 rigid atoms, others: [33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 241 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061488 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061488 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061488/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061488 Building REAL250005061489 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061489' /scratch/stefan/7916143/working/building/REAL250005061489 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061489 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061489/0 /scratch/stefan/7916143/working/building/REAL250005061489 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/613 `/scratch/stefan/7916143/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(O)C1CC1) `REAL250005061489.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061489 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 18, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 34, 45, 45, 66, 66, 81, 81, 87, 87, 34, 34, 34, 34, 18, 18, 5, 1, 45, 45, 45, 81, 243, 87, 87, 87, 87, 87] 261 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 599 number of broken/clashed sets: 164 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061489 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [49, 36, 49, 77, 87, 87, 87, 87, 87, 87, 87, 87, 21, 36, 8, 21, 1, 8, 1, 1, 1, 49, 49, 49, 49, 77, 77, 87, 87, 36, 36, 36, 8, 24, 1, 1, 1, 1, 1] 261 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: 369 number of broken/clashed sets: 164 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061489 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061489 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061489/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061489 Building REAL250005061490 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061490' /scratch/stefan/7916143/working/building/REAL250005061490 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061490 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061490/0 /scratch/stefan/7916143/working/building/REAL250005061490 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/614 `/scratch/stefan/7916143/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061490.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061490 none C=CCC(C)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 177, 123, 177, 82, 123, 65, 82, 22, 62, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 177, 177, 177, 177, 82, 82, 82, 65, 65, 65, 65, 22, 22, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 878 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061490 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061490 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061490/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061490 Building REAL250005061491 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061491' /scratch/stefan/7916143/working/building/REAL250005061491 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061491 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061491/0 /scratch/stefan/7916143/working/building/REAL250005061491 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/615 `/scratch/stefan/7916143/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC1F) `REAL250005061491.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061491 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [61, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 64, 102, 101, 146, 146, 170, 170, 170, 64, 64, 64, 64, 24, 24, 7, 1, 102, 102, 102, 170, 170, 170, 170] 170 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 625 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061491 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [58, 24, 58, 121, 167, 167, 167, 170, 170, 170, 170, 170, 8, 24, 1, 8, 1, 1, 1, 1, 58, 58, 58, 58, 121, 121, 167, 170, 24, 24, 24, 1, 1, 1, 1] 170 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 665 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061491 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061491 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061491/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061491 Building REAL250005061492 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061492' /scratch/stefan/7916143/working/building/REAL250005061492 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061492 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061492/0 /scratch/stefan/7916143/working/building/REAL250005061492 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/616 `/scratch/stefan/7916143/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H](C)[NH+](C)C) `REAL250005061492.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061492 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H](C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 9, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 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, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 8, 8, 4, 1, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 49 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061492 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061492/1 /scratch/stefan/7916143/working/building/REAL250005061492 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/617 `/scratch/stefan/7916143/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H](C)N(C)C) `REAL250005061492.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061492/1/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: REAL250005061492 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H](C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 10, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 17, 20, 20, 26, 26, 27, 27, 27, 27, 27, 17, 17, 17, 17, 12, 12, 4, 1, 20, 20, 20, 27, 27, 27, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061492 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061492 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061492/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061492/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061492 Building REAL250005061493 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061493' /scratch/stefan/7916143/working/building/REAL250005061493 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061493 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061493/0 /scratch/stefan/7916143/working/building/REAL250005061493 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/618 `/scratch/stefan/7916143/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CCF) `REAL250005061493.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061493 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 27, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 81, 124, 123, 172, 172, 201, 201, 81, 81, 81, 81, 27, 27, 5, 1, 124, 124, 124, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 26] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 804 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061493 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061493 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061493/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061493 Building REAL250005061494 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061494' /scratch/stefan/7916143/working/building/REAL250005061494 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061494 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061494/0 /scratch/stefan/7916143/working/building/REAL250005061494 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/619 `/scratch/stefan/7916143/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(O)COC1) `REAL250005061494.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061494 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(O)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 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 204 conformations in input total number of sets (complete confs): 204 using faster count positions algorithm for large data unique positions, atoms: [34, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 34, 45, 45, 57, 57, 68, 68, 68, 68, 34, 34, 34, 34, 16, 16, 4, 1, 45, 45, 45, 204, 68, 68, 68, 68] 204 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 462 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061494 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(O)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 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 204 conformations in input total number of sets (complete confs): 204 using faster count positions algorithm for large data unique positions, atoms: [31, 16, 31, 53, 68, 68, 68, 68, 68, 68, 68, 68, 6, 16, 1, 6, 1, 1, 1, 1, 1, 31, 31, 31, 31, 53, 53, 68, 68, 16, 16, 16, 6, 1, 1, 1, 1] 204 rigid atoms, others: [33, 34, 35, 36, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 281 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061494 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061494 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061494/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061494 Building REAL250005061495 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061495' /scratch/stefan/7916143/working/building/REAL250005061495 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061495 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061495/0 /scratch/stefan/7916143/working/building/REAL250005061495 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/620 `/scratch/stefan/7916143/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1)=C1CC1) `REAL250005061495.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061495 none CC(C(=O)N(C)C(C)CNC(=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', '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', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 99, 72, 99, 63, 72, 34, 63, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 72, 72, 72, 63, 63, 63, 63, 34, 34, 10, 1, 131, 131, 131, 131] 131 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 494 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061495 none CC(C(=O)N(C)C(C)CNC(=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', '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', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 7, 7, 19, 19, 28, 28, 70, 117, 117, 117, 131, 131, 131, 131, 131, 1, 1, 1, 2, 2, 2, 19, 19, 19, 28, 28, 28, 28, 70, 70, 117, 131, 1, 1, 1, 1] 131 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 18, 19, 20] set([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]) total number of confs: 460 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061495 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061495 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061495/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061495 Building REAL250005061496 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061496' /scratch/stefan/7916143/working/building/REAL250005061496 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061496 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061496/0 /scratch/stefan/7916143/working/building/REAL250005061496 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/621 `/scratch/stefan/7916143/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CC1C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061496.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061496 none CCC1CC1C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 42, 42, 100, 183, 183, 183, 189, 189, 189, 189, 189, 3, 3, 3, 3, 3, 1, 1, 1, 1, 29, 29, 29, 42, 42, 42, 42, 100, 100, 183, 189] 201 rigid atoms, others: [1, 2, 3, 4, 5, 26, 27, 28, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 663 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061496 none CCC1CC1C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 189, 139, 75, 139, 54, 75, 18, 52, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 189, 189, 189, 189, 75, 75, 75, 54, 54, 54, 54, 18, 18, 4, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 744 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061496 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061496 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061496/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061496 Building REAL250005061497 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061497' /scratch/stefan/7916143/working/building/REAL250005061497 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061497 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061497/0 /scratch/stefan/7916143/working/building/REAL250005061497 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/622 `/scratch/stefan/7916143/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC1(O)CC1) `REAL250005061497.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061497 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 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: [48, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 51, 76, 76, 125, 125, 179, 201, 201, 201, 51, 51, 51, 51, 19, 19, 4, 1, 76, 76, 76, 179, 179, 603, 201, 201, 201, 201] 603 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1424 number of broken/clashed sets: 222 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061497 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CC1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 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: [98, 56, 98, 154, 201, 201, 201, 201, 201, 201, 201, 201, 28, 56, 8, 28, 1, 1, 1, 1, 1, 98, 98, 98, 98, 154, 154, 201, 201, 56, 56, 56, 8, 8, 6, 1, 1, 1, 1] 603 rigid atoms, others: [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, 32, 33, 34]) total number of confs: 825 number of broken/clashed sets: 222 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061497 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061497 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061497/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061497 Building REAL250005061498 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061498' /scratch/stefan/7916143/working/building/REAL250005061498 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061498 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061498/0 /scratch/stefan/7916143/working/building/REAL250005061498 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/623 `/scratch/stefan/7916143/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C=CCF) `REAL250005061498.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061498 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C=CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 52, 90, 90, 138, 138, 189, 189, 201, 52, 52, 52, 52, 17, 17, 4, 1, 90, 90, 90, 189, 189, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 747 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061498 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061498 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061498/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061498 Building REAL250005061499 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061499' /scratch/stefan/7916143/working/building/REAL250005061499 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061499 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061499/0 /scratch/stefan/7916143/working/building/REAL250005061499 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/624 `/scratch/stefan/7916143/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061499.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061499 none C#CCCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 182, 138, 83, 138, 64, 83, 19, 60, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 191, 191, 191, 182, 182, 83, 83, 83, 64, 64, 64, 64, 19, 19, 4, 1] 191 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: 769 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061499 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061499 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061499/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061499 Building REAL250005061500 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061500' /scratch/stefan/7916143/working/building/REAL250005061500 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061500 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061500/0 /scratch/stefan/7916143/working/building/REAL250005061500 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/625 `/scratch/stefan/7916143/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CN1CCC1) `REAL250005061500.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061500 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CN1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 10, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 55, 90, 90, 123, 123, 182, 201, 201, 201, 55, 55, 55, 55, 20, 20, 4, 1, 90, 90, 90, 182, 182, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 796 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061500 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CN1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 10, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 105, 155, 201, 201, 201, 201, 201, 201, 201, 201, 28, 66, 6, 28, 1, 1, 1, 1, 1, 105, 105, 105, 105, 155, 155, 201, 201, 66, 66, 66, 6, 6, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 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: 797 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061500 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061500/1 /scratch/stefan/7916143/working/building/REAL250005061500 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/626 `/scratch/stefan/7916143/working/3D/626' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C[NH+]1CCC1) `REAL250005061500.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061500 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C[NH+]1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 9, 6, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 13, 13, 15, 15, 15, 16, 16, 16, 16, 12, 12, 12, 12, 8, 8, 5, 1, 13, 13, 13, 15, 15, 16, 16, 16, 16, 16, 16] 16 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 66 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061500 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C[NH+]1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 9, 6, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 16, 16, 16, 16, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 1] 16 rigid atoms, others: [35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 59 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061500 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061500 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061500/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061500/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061500 Building REAL250005061501 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061501' /scratch/stefan/7916143/working/building/REAL250005061501 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061501 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061501/0 /scratch/stefan/7916143/working/building/REAL250005061501 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/627 `/scratch/stefan/7916143/working/3D/627' -> `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)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061501.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061501 none C#C[C@H]1C[C@H]1C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 23, 23, 53, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 15, 15, 15, 23, 23, 23, 23, 53, 53, 83, 83] 83 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 307 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061501 none C#C[C@H]1C[C@H]1C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 83, 79, 83, 56, 79, 43, 56, 16, 42, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 83, 83, 83, 56, 56, 56, 43, 43, 43, 43, 16, 16, 5, 1] 83 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: 314 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061501 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061501 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061501/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061501 Building REAL250005061502 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061502' /scratch/stefan/7916143/working/building/REAL250005061502 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061502 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061502/0 /scratch/stefan/7916143/working/building/REAL250005061502 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/628 `/scratch/stefan/7916143/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1C2CCC21) `REAL250005061502.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061502 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1C2CCC21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 74, 116, 116, 165, 165, 201, 201, 201, 201, 74, 74, 74, 74, 28, 28, 6, 1, 116, 116, 116, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 749 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061502 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1C2CCC21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 134, 200, 200, 200, 201, 201, 201, 201, 201, 8, 21, 1, 8, 1, 1, 1, 1, 1, 53, 53, 53, 53, 134, 134, 200, 201, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 773 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061502 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061502 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061502/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061502 Building REAL250005061503 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061503' /scratch/stefan/7916143/working/building/REAL250005061503 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061503 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061503/0 /scratch/stefan/7916143/working/building/REAL250005061503 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/629 `/scratch/stefan/7916143/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC1C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061503.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061503 none C=C1CCC1C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 27, 27, 63, 101, 101, 101, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 27, 27, 27, 27, 63, 63, 101, 110] 110 rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 22, 23, 24, 25, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 390 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061503 none C=C1CCC1C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 110, 90, 65, 90, 51, 65, 31, 51, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 110, 110, 110, 65, 65, 65, 51, 51, 51, 51, 31, 31, 11, 1] 110 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: 404 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061503 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061503 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061503/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061503 Building REAL250005061504 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061504' /scratch/stefan/7916143/working/building/REAL250005061504 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061504 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061504/0 /scratch/stefan/7916143/working/building/REAL250005061504 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/630 `/scratch/stefan/7916143/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1[C@H](C)[C@@H]1C) `REAL250005061504.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061504 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1[C@H](C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 7, 5, 5, 7, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 60, 97, 97, 159, 159, 201, 201, 201, 201, 201, 201, 60, 60, 60, 60, 19, 19, 4, 1, 97, 97, 97, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 728 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061504 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1[C@H](C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 7, 5, 5, 7, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 70, 145, 200, 200, 200, 201, 201, 201, 201, 201, 8, 29, 1, 8, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 145, 145, 200, 201, 29, 29, 29, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 787 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061504 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061504 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061504/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061504 Building REAL250005061505 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061505' /scratch/stefan/7916143/working/building/REAL250005061505 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061505 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061505/0 /scratch/stefan/7916143/working/building/REAL250005061505 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/631 `/scratch/stefan/7916143/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H](C)[NH+](C)C) `REAL250005061505.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061505 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H](C)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 9, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 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, 6, 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, 6, 6, 4, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 7 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 27 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061505 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061505/1 /scratch/stefan/7916143/working/building/REAL250005061505 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/632 `/scratch/stefan/7916143/working/3D/632' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H](C)N(C)C) `REAL250005061505.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061505/1/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: REAL250005061505 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H](C)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 10, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 16, 20, 20, 29, 29, 29, 29, 29, 29, 29, 16, 16, 16, 16, 9, 9, 3, 1, 20, 20, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29] 29 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061505 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061505 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061505/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061505/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061505 Building REAL250005061506 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061506' /scratch/stefan/7916143/working/building/REAL250005061506 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061506 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061506/0 /scratch/stefan/7916143/working/building/REAL250005061506 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/633 `/scratch/stefan/7916143/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC=CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061506.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061506 none CC=CC=CC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 145, 85, 145, 67, 85, 20, 64, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 189, 189, 85, 85, 85, 67, 67, 67, 67, 20, 20, 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: 726 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061506 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061506 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061506/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061506 Building REAL250005061507 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061507' /scratch/stefan/7916143/working/building/REAL250005061507 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061507 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061507/0 /scratch/stefan/7916143/working/building/REAL250005061507 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/634 `/scratch/stefan/7916143/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC=CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061507.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061507 none COCC=CC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 139, 139, 91, 51, 91, 49, 51, 21, 49, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 200, 139, 139, 51, 51, 51, 49, 49, 49, 49, 21, 21, 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: 830 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061507 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061507 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061507/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061507 Building REAL250005061508 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061508' /scratch/stefan/7916143/working/building/REAL250005061508 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061508 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061508/0 /scratch/stefan/7916143/working/building/REAL250005061508 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/635 `/scratch/stefan/7916143/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(C)COC1) `REAL250005061508.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061508 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(C)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 12, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [53, 24, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 55, 75, 75, 107, 107, 107, 107, 107, 107, 55, 55, 55, 55, 24, 24, 8, 1, 75, 75, 75, 107, 107, 107, 107, 107, 107, 107] 107 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 399 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061508 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(C)COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 12, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 20, 63, 104, 104, 104, 107, 107, 107, 107, 107, 4, 6, 1, 4, 1, 1, 1, 1, 1, 20, 20, 20, 20, 63, 63, 104, 107, 6, 6, 6, 2, 2, 2, 1, 1, 1, 1] 107 rigid atoms, others: [35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 393 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061508 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061508 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061508/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061508 Building REAL250005061509 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061509' /scratch/stefan/7916143/working/building/REAL250005061509 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061509 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061509/0 /scratch/stefan/7916143/working/building/REAL250005061509 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/636 `/scratch/stefan/7916143/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCO1) `REAL250005061509.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061509 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [39, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 55, 55, 65, 65, 72, 72, 72, 39, 39, 39, 39, 17, 17, 4, 1, 55, 55, 55, 72, 72, 72, 72, 72] 72 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 272 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061509 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [35, 20, 35, 55, 72, 72, 72, 72, 72, 72, 72, 72, 7, 20, 1, 7, 1, 1, 1, 1, 35, 35, 35, 35, 55, 55, 72, 72, 20, 20, 20, 1, 1, 1, 1, 1] 72 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 279 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061509 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061509 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061509/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061509 Building REAL250005061510 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061510' /scratch/stefan/7916143/working/building/REAL250005061510 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061510 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061510/0 /scratch/stefan/7916143/working/building/REAL250005061510 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/637 `/scratch/stefan/7916143/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CCN=[N+]=[N-]) `REAL250005061510.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061510 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CCN=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 36, 59, 59, 85, 85, 108, 126, 201, 201, 36, 36, 36, 36, 12, 12, 4, 1, 59, 59, 59, 108, 108, 126, 126] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 662 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061510 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061510 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061510/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061510 Building REAL250005061511 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061511' /scratch/stefan/7916143/working/building/REAL250005061511 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061511 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061511/0 /scratch/stefan/7916143/working/building/REAL250005061511 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/638 `/scratch/stefan/7916143/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061511.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061511 none C#CCOCC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 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, 7, 4, 7, 6, 7, 7, 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, 160, 122, 86, 49, 86, 44, 49, 19, 44, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 122, 122, 49, 49, 49, 44, 44, 44, 44, 19, 19, 4, 1] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 808 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061511 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061511 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061511/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061511 Building REAL250005061512 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061512' /scratch/stefan/7916143/working/building/REAL250005061512 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061512 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061512/0 /scratch/stefan/7916143/working/building/REAL250005061512 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/639 `/scratch/stefan/7916143/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(C)(C)O) `REAL250005061512.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061512 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [15, 10, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 15, 16, 16, 16, 16, 17, 17, 17, 15, 15, 15, 15, 10, 10, 3, 1, 16, 16, 16, 17, 17, 17, 17, 17, 17, 51] 51 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061512 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061512 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061512/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061512 Building REAL250005061513 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061513' /scratch/stefan/7916143/working/building/REAL250005061513 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061513 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061513/0 /scratch/stefan/7916143/working/building/REAL250005061513 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/640 `/scratch/stefan/7916143/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061513.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061513 none CC1=CC1C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [1, 1, 1, 1, 1, 8, 8, 22, 22, 31, 31, 77, 124, 124, 124, 133, 133, 133, 133, 133, 2, 2, 2, 1, 1, 22, 22, 22, 31, 31, 31, 31, 77, 77, 124, 133] 133 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 475 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061513 none CC1=CC1C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [133, 133, 133, 103, 75, 103, 64, 75, 39, 64, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 75, 75, 75, 64, 64, 64, 64, 39, 39, 11, 1] 133 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: 479 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061513 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061513 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061513/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061513 Building REAL250005061514 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061514' /scratch/stefan/7916143/working/building/REAL250005061514 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061514 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061514/0 /scratch/stefan/7916143/working/building/REAL250005061514 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/641 `/scratch/stefan/7916143/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(=O)N(C)C) `REAL250005061514.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061514 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 3, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061514 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061514 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061514/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061514 Building REAL250005061515 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061515' /scratch/stefan/7916143/working/building/REAL250005061515 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061515 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061515/0 /scratch/stefan/7916143/working/building/REAL250005061515 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/642 `/scratch/stefan/7916143/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC=CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061515.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061515 none CSC=CC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [176, 161, 161, 117, 63, 117, 57, 63, 21, 57, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 176, 176, 176, 161, 161, 63, 63, 63, 57, 57, 57, 57, 21, 21, 4, 1] 176 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: 599 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061515 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061515 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061515/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061515 Building REAL250005061516 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061516' /scratch/stefan/7916143/working/building/REAL250005061516 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061516 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061516/0 /scratch/stefan/7916143/working/building/REAL250005061516 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/643 `/scratch/stefan/7916143/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(O)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061516.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061516 none CCC(C)(O)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 9, 8, 9, 7, 8, 6, 7, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 9, 9, 9, 27, 8, 8, 8, 7, 7, 7, 7, 6, 6, 2, 1] 30 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: 71 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061516 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061516 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061516/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061516 Building REAL250005061517 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061517' /scratch/stefan/7916143/working/building/REAL250005061517 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005061517 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061517/0 /scratch/stefan/7916143/working/building/REAL250005061517 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/644 `/scratch/stefan/7916143/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061517.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061517 none CC[N@H+](C)CC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 20, 15, 20, 20, 14, 12, 14, 12, 12, 11, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 20, 20, 20, 15, 15, 12, 12, 12, 12, 12, 12, 12, 11, 11, 7, 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: 89 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061517 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061517/1 /scratch/stefan/7916143/working/building/REAL250005061517 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/645 `/scratch/stefan/7916143/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061517.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061517/1/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: REAL250005061517 none CC[N@@H+](C)CC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 20, 15, 20, 20, 14, 12, 14, 12, 12, 11, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 20, 20, 20, 15, 15, 12, 12, 12, 12, 12, 12, 12, 11, 11, 7, 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: 89 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061517 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `2' /scratch/stefan/7916143/working/building/REAL250005061517/2 /scratch/stefan/7916143/working/building/REAL250005061517 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 2 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/646 `/scratch/stefan/7916143/working/3D/646' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061517.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005061517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061517/2/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: REAL250005061517 none CCN(C)CC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 176, 196, 125, 69, 125, 52, 69, 18, 49, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 196, 196, 196, 176, 176, 69, 69, 69, 52, 52, 52, 52, 18, 18, 4, 1] 201 rigid atoms, others: [41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 803 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061517 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061517 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061517/0.* 2: /scratch/stefan/7916143/working/building/REAL250005061517/2.* 1: /scratch/stefan/7916143/working/building/REAL250005061517/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061517 Building REAL250005061518 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061518' /scratch/stefan/7916143/working/building/REAL250005061518 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061518 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061518/0 /scratch/stefan/7916143/working/building/REAL250005061518 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/647 `/scratch/stefan/7916143/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C(=O)N(C)C(C)CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061518.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061518 none C=C1CC(C(=O)N(C)C(C)CNC(=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', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 30, 30, 50, 50, 124, 190, 190, 190, 190, 190, 190, 190, 190, 1, 1, 1, 1, 1, 1, 30, 30, 30, 50, 50, 50, 50, 124, 124, 190, 190, 1, 1] 190 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 20, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061518 none C=C1CC(C(=O)N(C)C(C)CNC(=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', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 158, 102, 158, 72, 102, 21, 69, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 190, 190, 190, 190, 190, 190, 102, 102, 102, 72, 72, 72, 72, 21, 21, 5, 1, 190, 190] 190 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: 687 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061518 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061518 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061518/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061518 Building REAL250005061519 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061519' /scratch/stefan/7916143/working/building/REAL250005061519 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061519 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061519/0 /scratch/stefan/7916143/working/building/REAL250005061519 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/648 `/scratch/stefan/7916143/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCC1F) `REAL250005061519.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061519 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 78, 123, 123, 181, 181, 201, 201, 201, 201, 78, 78, 78, 78, 24, 24, 5, 1, 123, 123, 123, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 742 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061519 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CCC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 65, 146, 201, 201, 201, 201, 201, 201, 201, 201, 6, 24, 1, 6, 1, 1, 1, 1, 1, 65, 65, 65, 65, 146, 146, 201, 201, 24, 24, 24, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 800 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061519 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061519 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061519/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061519 Building REAL250005061520 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061520' /scratch/stefan/7916143/working/building/REAL250005061520 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061520 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061520/0 /scratch/stefan/7916143/working/building/REAL250005061520 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/649 `/scratch/stefan/7916143/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CNC=N1) `REAL250005061520.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061520 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CNC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 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: [39, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 63, 63, 88, 88, 108, 108, 108, 108, 41, 41, 41, 41, 15, 15, 4, 1, 63, 63, 63, 108, 108, 108] 108 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 353 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061520 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CNC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 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: [54, 29, 54, 81, 108, 108, 108, 108, 108, 108, 108, 108, 12, 29, 1, 12, 1, 1, 1, 1, 1, 54, 54, 54, 54, 81, 81, 108, 108, 29, 29, 29, 1, 1, 1] 108 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 432 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061520 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061520/1 /scratch/stefan/7916143/working/building/REAL250005061520 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/650 `/scratch/stefan/7916143/working/3D/650' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CN=CN1) `REAL250005061520.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061520 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CN=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [34, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 55, 55, 82, 82, 94, 94, 94, 94, 35, 35, 35, 35, 12, 12, 4, 1, 55, 55, 55, 94, 94, 94] 94 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 314 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061520 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CN=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [36, 16, 36, 72, 94, 94, 94, 94, 94, 94, 94, 94, 10, 16, 1, 10, 1, 1, 1, 1, 1, 36, 36, 36, 36, 72, 72, 94, 94, 16, 16, 16, 1, 1, 1] 94 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 375 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061520 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061520 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061520/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061520/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061520 Building REAL250005061521 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061521' /scratch/stefan/7916143/working/building/REAL250005061521 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061521 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061521/0 /scratch/stefan/7916143/working/building/REAL250005061521 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/651 `/scratch/stefan/7916143/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CCCO1) `REAL250005061521.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061521 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 60, 96, 96, 162, 162, 201, 201, 201, 201, 60, 60, 60, 60, 20, 20, 4, 1, 96, 96, 96, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 637 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061521 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 38, 84, 148, 201, 201, 201, 201, 201, 201, 201, 201, 12, 38, 1, 12, 1, 1, 1, 1, 1, 84, 84, 84, 84, 148, 148, 201, 201, 38, 38, 38, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 816 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061521 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061521 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061521/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061521 Building REAL250005061522 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061522' /scratch/stefan/7916143/working/building/REAL250005061522 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061522 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061522/0 /scratch/stefan/7916143/working/building/REAL250005061522 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/652 `/scratch/stefan/7916143/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](O)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061522.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061522 none CCC[C@H](O)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 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] 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: [162, 162, 129, 92, 129, 129, 56, 92, 40, 56, 16, 40, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 162, 162, 162, 387, 56, 56, 56, 40, 40, 40, 40, 16, 16, 4, 1] 486 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: 1108 number of broken/clashed sets: 145 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061522 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061522 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061522/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061522 Building REAL250005061523 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061523' /scratch/stefan/7916143/working/building/REAL250005061523 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061523 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061523/0 /scratch/stefan/7916143/working/building/REAL250005061523 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/653 `/scratch/stefan/7916143/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](O)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061523.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061523 none CC(C)[C@H](O)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 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] 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: [104, 92, 104, 73, 92, 92, 49, 73, 41, 49, 19, 41, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 104, 104, 276, 49, 49, 49, 41, 41, 41, 41, 19, 19, 5, 1] 312 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: 738 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061523 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061523 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061523/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061523 Building REAL250005061524 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061524' /scratch/stefan/7916143/working/building/REAL250005061524 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061524 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061524/0 /scratch/stefan/7916143/working/building/REAL250005061524 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/654 `/scratch/stefan/7916143/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC=CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061524.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061524 none CCOC=CC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 169, 169, 108, 59, 108, 51, 59, 19, 51, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 169, 169, 59, 59, 59, 51, 51, 51, 51, 19, 19, 4, 1] 201 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 666 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061524 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061524 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061524/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061524 Building REAL250005061525 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061525' /scratch/stefan/7916143/working/building/REAL250005061525 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061525 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061525/0 /scratch/stefan/7916143/working/building/REAL250005061525 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/655 `/scratch/stefan/7916143/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H](C)O) `REAL250005061525.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061525 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [32, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 33, 42, 42, 53, 53, 53, 53, 53, 33, 33, 33, 33, 16, 16, 5, 1, 42, 42, 42, 53, 53, 53, 159] 159 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 366 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061525 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061525 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061525/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061525 Building REAL250005061526 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061526' /scratch/stefan/7916143/working/building/REAL250005061526 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061526 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061526/0 /scratch/stefan/7916143/working/building/REAL250005061526 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/656 `/scratch/stefan/7916143/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C=CCO) `REAL250005061526.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061526 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C=CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [39, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 75, 75, 122, 122, 187, 187, 201, 41, 41, 41, 41, 17, 17, 4, 1, 75, 75, 75, 187, 187, 201, 201, 603] 603 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1352 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061526 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061526 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061526/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061526 Building REAL250005061527 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061527' /scratch/stefan/7916143/working/building/REAL250005061527 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061527 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061527/0 /scratch/stefan/7916143/working/building/REAL250005061527 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/657 `/scratch/stefan/7916143/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061527.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061527 none COC(C)(C)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 13, 14, 11, 13, 8, 11, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13, 13, 11, 11, 11, 11, 8, 8, 4, 1] 14 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: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061527 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061527 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061527/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061527 Building REAL250005061528 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061528' /scratch/stefan/7916143/working/building/REAL250005061528 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061528 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061528/0 /scratch/stefan/7916143/working/building/REAL250005061528 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/658 `/scratch/stefan/7916143/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CCCCO) `REAL250005061528.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061528 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CCCCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 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: [37, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 71, 71, 106, 106, 145, 164, 201, 201, 39, 39, 39, 39, 14, 14, 4, 1, 71, 71, 71, 145, 145, 164, 164, 201, 201, 201, 201, 603] 603 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1501 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061528 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061528 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061528/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061528 Building REAL250005061529 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061529' /scratch/stefan/7916143/working/building/REAL250005061529 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061529 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061529/0 /scratch/stefan/7916143/working/building/REAL250005061529 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/659 `/scratch/stefan/7916143/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(CO)CC1) `REAL250005061529.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061529 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 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: [61, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 106, 106, 164, 164, 186, 201, 186, 186, 65, 65, 65, 65, 22, 22, 4, 1, 106, 106, 106, 201, 201, 603, 186, 186, 186, 186] 603 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1361 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061529 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 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, 10, 26, 81, 179, 179, 179, 186, 186, 186, 186, 186, 4, 10, 1, 4, 1, 1, 10, 1, 1, 26, 26, 26, 26, 81, 81, 179, 186, 10, 10, 10, 10, 10, 30, 1, 1, 1, 1] 603 rigid atoms, others: [35, 36, 37, 38, 14, 16, 17, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 682 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061529 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061529 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061529/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061529 Building REAL250005061530 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061530' /scratch/stefan/7916143/working/building/REAL250005061530 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061530 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061530/0 /scratch/stefan/7916143/working/building/REAL250005061530 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/660 `/scratch/stefan/7916143/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(F)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061530.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061530 none COC(F)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 58, 41, 58, 26, 41, 24, 26, 17, 24, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 60, 60, 60, 58, 26, 26, 26, 24, 24, 24, 24, 17, 17, 4, 1] 60 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 241 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061530 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061530 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061530/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061530 Building REAL250005061531 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061531' /scratch/stefan/7916143/working/building/REAL250005061531 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061531 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061531/0 /scratch/stefan/7916143/working/building/REAL250005061531 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/661 `/scratch/stefan/7916143/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C12CC1CC2) `REAL250005061531.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061531 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C12CC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [58, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 59, 90, 90, 116, 116, 118, 118, 118, 118, 59, 59, 59, 59, 29, 29, 9, 1, 90, 90, 90, 118, 118, 118, 118, 118, 118, 118] 118 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 421 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061531 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C12CC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 9, 26, 69, 107, 107, 107, 118, 118, 118, 118, 118, 4, 9, 1, 4, 1, 1, 1, 1, 1, 26, 26, 26, 26, 69, 69, 107, 118, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1] 118 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 425 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061531 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061531 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061531/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061531 Building REAL250005061532 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061532' /scratch/stefan/7916143/working/building/REAL250005061532 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061532 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061532/0 /scratch/stefan/7916143/working/building/REAL250005061532 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/662 `/scratch/stefan/7916143/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@H](C)CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061532.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061532 none C=C[C@H](C)CC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 181, 201, 201, 142, 86, 142, 68, 86, 22, 65, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 181, 181, 86, 86, 86, 68, 68, 68, 68, 22, 22, 4, 1] 201 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 832 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061532 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061532 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061532/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061532 Building REAL250005061533 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061533' /scratch/stefan/7916143/working/building/REAL250005061533 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061533 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061533/0 /scratch/stefan/7916143/working/building/REAL250005061533 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/663 `/scratch/stefan/7916143/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C=CC1CC1) `REAL250005061533.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061533 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C=CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 71, 71, 105, 105, 160, 160, 201, 201, 39, 39, 39, 39, 14, 14, 4, 1, 71, 71, 71, 160, 160, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 741 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061533 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C=CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 78, 119, 172, 201, 201, 201, 201, 201, 201, 201, 201, 46, 78, 9, 45, 9, 1, 1, 1, 1, 119, 119, 119, 119, 172, 172, 201, 201, 78, 78, 78, 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: 800 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061533 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061533 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061533/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061533 Building REAL250005061534 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061534' /scratch/stefan/7916143/working/building/REAL250005061534 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061534 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061534/0 /scratch/stefan/7916143/working/building/REAL250005061534 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/664 `/scratch/stefan/7916143/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(CC)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061534.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061534 none CC=C(CC)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 139, 190, 201, 70, 139, 55, 70, 20, 54, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 190, 190, 190, 190, 201, 201, 201, 201, 201, 70, 70, 70, 55, 55, 55, 55, 20, 20, 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: 747 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061534 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061534 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061534/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061534 Building REAL250005061535 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061535' /scratch/stefan/7916143/working/building/REAL250005061535 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061535 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061535/0 /scratch/stefan/7916143/working/building/REAL250005061535 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/665 `/scratch/stefan/7916143/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061535.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061535 none C=CC(C)(O)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 26, 31, 31, 22, 26, 20, 22, 13, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 93, 22, 22, 22, 20, 20, 20, 20, 13, 13, 4, 1] 93 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: 232 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061535 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061535 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061535/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061535 Building REAL250005061536 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061536' /scratch/stefan/7916143/working/building/REAL250005061536 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061536 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061536/0 /scratch/stefan/7916143/working/building/REAL250005061536 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/666 `/scratch/stefan/7916143/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CCC1) `REAL250005061536.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061536 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [62, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 64, 102, 102, 157, 157, 157, 157, 157, 64, 64, 64, 64, 20, 20, 4, 1, 102, 102, 102, 157, 157, 157, 157, 157] 157 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 547 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061536 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [70, 35, 70, 117, 157, 157, 157, 157, 157, 157, 157, 157, 12, 35, 1, 12, 1, 1, 1, 1, 70, 70, 70, 70, 117, 117, 157, 157, 35, 35, 35, 1, 1, 1, 1, 1] 157 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 629 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061536 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061536 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061536/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061536 Building REAL250005061537 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061537' /scratch/stefan/7916143/working/building/REAL250005061537 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061537 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061537/0 /scratch/stefan/7916143/working/building/REAL250005061537 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/667 `/scratch/stefan/7916143/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061537.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061537 none CON=CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [156, 155, 155, 125, 71, 125, 54, 71, 16, 51, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 156, 156, 156, 155, 71, 71, 71, 54, 54, 54, 54, 16, 16, 4, 1] 156 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: 574 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061537 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061537 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061537/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061537 Building REAL250005061538 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061538' /scratch/stefan/7916143/working/building/REAL250005061538 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061538 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061538/0 /scratch/stefan/7916143/working/building/REAL250005061538 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/668 `/scratch/stefan/7916143/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(F)CC1) `REAL250005061538.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061538 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [56, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 59, 88, 88, 111, 111, 134, 134, 134, 59, 59, 59, 59, 20, 20, 4, 1, 88, 88, 88, 134, 134, 134, 134] 134 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 517 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061538 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [47, 23, 47, 95, 134, 134, 134, 134, 134, 134, 134, 134, 9, 23, 1, 9, 1, 1, 1, 1, 47, 47, 47, 47, 95, 95, 134, 134, 23, 23, 23, 1, 1, 1, 1] 134 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 525 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061538 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061538 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061538/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061538 Building REAL250005061539 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061539' /scratch/stefan/7916143/working/building/REAL250005061539 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061539 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061539/0 /scratch/stefan/7916143/working/building/REAL250005061539 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/669 `/scratch/stefan/7916143/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=NOCC1) `REAL250005061539.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061539 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=NOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 20, 27, 27, 33, 33, 34, 34, 34, 34, 20, 20, 20, 20, 12, 12, 4, 1, 27, 27, 27, 34, 34, 34, 34] 34 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061539 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=NOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 21, 28, 34, 34, 34, 34, 34, 34, 34, 34, 7, 16, 1, 7, 1, 1, 1, 1, 1, 21, 21, 21, 21, 28, 28, 34, 34, 16, 16, 16, 1, 1, 1, 1] 34 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061539 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061539 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061539/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061539 Building REAL250005061540 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061540' /scratch/stefan/7916143/working/building/REAL250005061540 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061540 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061540/0 /scratch/stefan/7916143/working/building/REAL250005061540 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/670 `/scratch/stefan/7916143/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC(C)(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061540.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061540 none C#CC(C)(C)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [36, 36, 36, 36, 36, 34, 36, 27, 34, 17, 27, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 36, 34, 34, 34, 27, 27, 27, 27, 17, 17, 8, 1] 36 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: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061540 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061540 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061540/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061540 Building REAL250005061541 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061541' /scratch/stefan/7916143/working/building/REAL250005061541 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061541 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061541/0 /scratch/stefan/7916143/working/building/REAL250005061541 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/671 `/scratch/stefan/7916143/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)COC1CC1) `REAL250005061541.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061541 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)COC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 12, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 30, 47, 47, 72, 72, 115, 166, 201, 201, 30, 30, 30, 30, 12, 12, 4, 1, 47, 47, 47, 115, 115, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061541 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)COC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 12, 5, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 0 hydrogens 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, 99, 129, 162, 201, 201, 201, 201, 201, 201, 201, 201, 69, 99, 24, 69, 6, 1, 1, 1, 1, 129, 129, 129, 129, 162, 162, 201, 201, 99, 99, 99, 24, 24, 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: 792 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061541 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061541 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061541/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061541 Building REAL250005061542 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061542' /scratch/stefan/7916143/working/building/REAL250005061542 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061542 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061542/0 /scratch/stefan/7916143/working/building/REAL250005061542 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/672 `/scratch/stefan/7916143/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=NC=CN1) `REAL250005061542.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061542 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=NC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [41, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 42, 53, 53, 62, 62, 62, 62, 62, 62, 42, 42, 42, 42, 24, 24, 9, 1, 53, 53, 53, 62, 62, 62] 62 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061542 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=NC=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [32, 18, 32, 56, 65, 65, 65, 65, 65, 65, 65, 65, 10, 18, 1, 10, 1, 1, 1, 1, 1, 32, 32, 32, 32, 56, 56, 65, 65, 18, 18, 18, 1, 1, 1] 65 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 252 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061542 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061542 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061542/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061542 Building REAL250005061543 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061543' /scratch/stefan/7916143/working/building/REAL250005061543 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061543 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061543/0 /scratch/stefan/7916143/working/building/REAL250005061543 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/673 `/scratch/stefan/7916143/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC=CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061543.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061543 none CCCC=CC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 176, 131, 131, 84, 41, 84, 36, 41, 16, 36, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 176, 176, 131, 131, 41, 41, 41, 36, 36, 36, 36, 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: 879 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061543 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061543 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061543/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061543 Building REAL250005061544 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061544' /scratch/stefan/7916143/working/building/REAL250005061544 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061544 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061544/0 /scratch/stefan/7916143/working/building/REAL250005061544 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/674 `/scratch/stefan/7916143/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061544.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061544 none CC=C(F)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 126, 147, 88, 126, 70, 88, 39, 69, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 88, 88, 88, 70, 70, 70, 70, 39, 39, 11, 1] 147 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: 548 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061544 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061544 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061544/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061544 Building REAL250005061545 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061545' /scratch/stefan/7916143/working/building/REAL250005061545 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061545 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061545/0 /scratch/stefan/7916143/working/building/REAL250005061545 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/675 `/scratch/stefan/7916143/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CO)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061545.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061545 none CCC(CO)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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 525 conformations in input total number of sets (complete confs): 525 using faster count positions algorithm for large data unique positions, atoms: [162, 147, 100, 147, 168, 63, 100, 46, 63, 15, 45, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 170, 170, 170, 170, 170, 147, 168, 168, 504, 63, 63, 63, 46, 46, 46, 46, 15, 15, 4, 1] 525 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: 1426 number of broken/clashed sets: 222 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061545 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061545 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061545/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061545 Building REAL250005061546 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061546' /scratch/stefan/7916143/working/building/REAL250005061546 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061546 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061546/0 /scratch/stefan/7916143/working/building/REAL250005061546 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/676 `/scratch/stefan/7916143/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061546.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061546 none CC(CO)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 510 conformations in input total number of sets (complete confs): 510 using faster count positions algorithm for large data unique positions, atoms: [167, 134, 167, 170, 81, 134, 60, 81, 21, 57, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 170, 170, 510, 81, 81, 81, 60, 60, 60, 60, 21, 21, 4, 1] 510 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: 1209 number of broken/clashed sets: 187 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061546 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061546 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061546/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061546 Building REAL250005061547 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061547' /scratch/stefan/7916143/working/building/REAL250005061547 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061547 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061547/0 /scratch/stefan/7916143/working/building/REAL250005061547 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/677 `/scratch/stefan/7916143/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CON=C1) `REAL250005061547.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061547 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CON=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [43, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 46, 72, 72, 117, 117, 201, 201, 201, 201, 46, 46, 46, 46, 15, 15, 4, 1, 72, 72, 72, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 591 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061547 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CON=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [65, 26, 65, 147, 201, 201, 201, 201, 201, 201, 201, 201, 11, 26, 1, 11, 1, 1, 1, 1, 1, 65, 65, 65, 65, 147, 147, 201, 201, 26, 26, 26, 1, 1] 201 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 829 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061547 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061547 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061547/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061547 Building REAL250005061548 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061548' /scratch/stefan/7916143/working/building/REAL250005061548 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061548 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061548/0 /scratch/stefan/7916143/working/building/REAL250005061548 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/678 `/scratch/stefan/7916143/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H]1C[C@H]1CF) `REAL250005061548.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061548 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H]1C[C@H]1CF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 51, 80, 80, 130, 130, 193, 193, 193, 193, 193, 201, 51, 51, 51, 51, 20, 20, 4, 1, 80, 80, 80, 193, 193, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 752 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061548 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H]1C[C@H]1CF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 47, 101, 185, 185, 185, 193, 193, 193, 193, 193, 8, 23, 1, 8, 1, 1, 1, 1, 1, 1, 9, 47, 47, 47, 47, 101, 101, 185, 193, 23, 23, 23, 1, 1, 9, 9] 201 rigid atoms, others: [34, 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, 36, 37]) total number of confs: 702 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061548 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061548 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061548/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061548 Building REAL250005061549 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061549' /scratch/stefan/7916143/working/building/REAL250005061549 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061549 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061549/0 /scratch/stefan/7916143/working/building/REAL250005061549 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/679 `/scratch/stefan/7916143/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)N(C)C(C)CNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005061549.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061549 none C#CC1(C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 11, 11, 21, 21, 65, 126, 126, 126, 135, 135, 135, 135, 135, 1, 1, 1, 11, 11, 11, 21, 21, 21, 21, 65, 65, 126, 135, 1, 1, 1, 1] 135 rigid atoms, others: [0, 1, 2, 3, 36, 35, 33, 34, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 478 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061549 none C#CC1(C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 112, 87, 112, 67, 87, 37, 67, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 135, 135, 135, 87, 87, 87, 67, 67, 67, 67, 37, 37, 10, 1, 135, 135, 135, 135] 135 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 510 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061549 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061549 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061549/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061549 Building REAL250005061550 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061550' /scratch/stefan/7916143/working/building/REAL250005061550 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061550 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061550/0 /scratch/stefan/7916143/working/building/REAL250005061550 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/680 `/scratch/stefan/7916143/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=COCC1) `REAL250005061550.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061550 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=COCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [48, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 51, 82, 82, 142, 142, 162, 162, 162, 162, 51, 51, 51, 51, 17, 17, 4, 1, 82, 82, 82, 162, 162, 162, 162, 162] 162 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 534 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061550 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=COCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [65, 25, 65, 121, 162, 162, 162, 162, 162, 162, 162, 162, 11, 25, 1, 11, 1, 1, 1, 1, 1, 65, 65, 65, 65, 121, 121, 162, 162, 25, 25, 25, 1, 1, 1, 1, 1] 162 rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 668 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061550 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061550 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061550/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061550 Building REAL250005061551 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061551' /scratch/stefan/7916143/working/building/REAL250005061551 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061551 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061551/0 /scratch/stefan/7916143/working/building/REAL250005061551 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/681 `/scratch/stefan/7916143/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H](C)O) `REAL250005061551.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061551 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [32, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 33, 42, 42, 53, 53, 53, 53, 53, 33, 33, 33, 33, 16, 16, 5, 1, 42, 42, 42, 53, 53, 53, 159] 159 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 366 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061551 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061551 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061551/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061551 Building REAL250005061552 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061552' /scratch/stefan/7916143/working/building/REAL250005061552 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061552 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061552/0 /scratch/stefan/7916143/working/building/REAL250005061552 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/682 `/scratch/stefan/7916143/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1C=CCC1) `REAL250005061552.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061552 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 1, 1, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [73, 27, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 76, 118, 118, 170, 170, 189, 189, 189, 189, 76, 76, 76, 76, 27, 27, 6, 1, 118, 118, 118, 189, 189, 189, 189, 189, 189, 189] 189 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 696 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061552 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 1, 1, 5, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [63, 22, 63, 133, 188, 188, 188, 189, 189, 189, 189, 189, 6, 22, 1, 6, 1, 1, 1, 1, 1, 63, 63, 63, 63, 133, 133, 188, 189, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1] 189 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 755 number of broken/clashed sets: 75 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061552 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061552 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061552/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061552 Building REAL250005061553 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061553' /scratch/stefan/7916143/working/building/REAL250005061553 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061553 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061553/0 /scratch/stefan/7916143/working/building/REAL250005061553 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/683 `/scratch/stefan/7916143/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061553.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061553 none CC(O)C(C)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 600 conformations in input total number of sets (complete confs): 600 using faster count positions algorithm for large data unique positions, atoms: [200, 160, 200, 124, 160, 81, 124, 58, 81, 21, 55, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 600, 160, 160, 160, 160, 81, 81, 81, 58, 58, 58, 58, 21, 21, 6, 1] 600 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: 1500 number of broken/clashed sets: 198 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061553 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061553 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061553/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061553 Building REAL250005061554 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061554' /scratch/stefan/7916143/working/building/REAL250005061554 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061554 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061554/0 /scratch/stefan/7916143/working/building/REAL250005061554 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/684 `/scratch/stefan/7916143/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061554.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061554 none C=C1CC1C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 22, 22, 29, 29, 70, 112, 112, 112, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 22, 22, 22, 29, 29, 29, 29, 70, 70, 112, 121] 121 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 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]) total number of confs: 423 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061554 none C=C1CC1C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 87, 67, 87, 56, 67, 33, 56, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 67, 67, 67, 56, 56, 56, 56, 33, 33, 9, 1] 121 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: 462 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061554 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061554 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061554/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061554 Building REAL250005061555 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061555' /scratch/stefan/7916143/working/building/REAL250005061555 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061555 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061555/0 /scratch/stefan/7916143/working/building/REAL250005061555 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/685 `/scratch/stefan/7916143/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061555.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061555 none CC(CF)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [191, 149, 191, 198, 89, 149, 63, 89, 23, 61, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 191, 191, 191, 191, 198, 198, 89, 89, 89, 63, 63, 63, 63, 23, 23, 4, 1] 198 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: 822 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061555 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061555 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061555/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061555 Building REAL250005061556 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061556' /scratch/stefan/7916143/working/building/REAL250005061556 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061556 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061556/0 /scratch/stefan/7916143/working/building/REAL250005061556 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/686 `/scratch/stefan/7916143/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061556.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061556 none C=C(C)CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 107, 65, 107, 48, 65, 18, 47, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 65, 65, 65, 48, 48, 48, 48, 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: 823 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061556 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061556 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061556/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061556 Building REAL250005061557 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061557' /scratch/stefan/7916143/working/building/REAL250005061557 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061557 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061557/0 /scratch/stefan/7916143/working/building/REAL250005061557 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/687 `/scratch/stefan/7916143/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061557.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061557 none CC(C)=C(C)C(=O)N(C)C(C)CNC(=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 82, 103, 63, 82, 55, 63, 29, 54, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 103, 103, 103, 103, 63, 63, 63, 55, 55, 55, 55, 29, 29, 9, 1] 103 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: 397 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061557 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061557 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061557/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061557 Building REAL250005061558 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061558' /scratch/stefan/7916143/working/building/REAL250005061558 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061558 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061558/0 /scratch/stefan/7916143/working/building/REAL250005061558 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/688 `/scratch/stefan/7916143/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061558.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061558 none CCCC(O)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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 486 conformations in input total number of sets (complete confs): 486 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 129, 92, 129, 56, 92, 41, 56, 16, 41, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 162, 162, 162, 129, 387, 56, 56, 56, 41, 41, 41, 41, 16, 16, 4, 1] 486 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: 1114 number of broken/clashed sets: 127 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061558 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061558 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061558/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061558 Building REAL250005061559 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061559' /scratch/stefan/7916143/working/building/REAL250005061559 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061559 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061559/0 /scratch/stefan/7916143/working/building/REAL250005061559 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/689 `/scratch/stefan/7916143/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061559.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061559 none CCC(O)CC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 196, 171, 196, 121, 72, 121, 53, 72, 19, 51, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 196, 588, 171, 171, 72, 72, 72, 53, 53, 53, 53, 19, 19, 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: 1432 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061559 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061559 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061559/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061559 Building REAL250005061560 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061560' /scratch/stefan/7916143/working/building/REAL250005061560 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061560 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061560/0 /scratch/stefan/7916143/working/building/REAL250005061560 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/690 `/scratch/stefan/7916143/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061560.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061560 none CC=CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 105, 82, 105, 68, 82, 42, 68, 11, 12, 1, 12, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 114, 82, 82, 82, 68, 68, 68, 68, 42, 42, 12, 1] 114 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 434 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061560 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061560 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061560/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061560 Building REAL250005061561 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061561' /scratch/stefan/7916143/working/building/REAL250005061561 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061561 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061561/0 /scratch/stefan/7916143/working/building/REAL250005061561 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/691 `/scratch/stefan/7916143/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(C)CC1F) `REAL250005061561.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061561 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(C)CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 28, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 53, 75, 75, 100, 100, 101, 101, 101, 101, 53, 53, 53, 53, 28, 28, 9, 1, 75, 75, 75, 101, 101, 101, 101, 101, 101] 101 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 398 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061561 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(C)CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 7, 18, 52, 98, 98, 98, 101, 101, 101, 101, 101, 3, 7, 1, 3, 1, 1, 1, 1, 1, 18, 18, 18, 18, 52, 52, 98, 101, 7, 7, 7, 2, 2, 2, 1, 1, 1] 101 rigid atoms, others: [35, 36, 37, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 379 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061561 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061561 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061561/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061561 Building REAL250005061562 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061562' /scratch/stefan/7916143/working/building/REAL250005061562 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061562 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061562/0 /scratch/stefan/7916143/working/building/REAL250005061562 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/692 `/scratch/stefan/7916143/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H]1C[C@@H](O)C1) `REAL250005061562.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061562 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H]1C[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 1 hydrogens need rotated 492 conformations in input total number of sets (complete confs): 492 using faster count positions algorithm for large data unique positions, atoms: [55, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 57, 88, 88, 137, 137, 164, 164, 164, 164, 164, 164, 57, 57, 57, 57, 23, 23, 8, 1, 88, 88, 88, 164, 164, 492, 164, 164] 492 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 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: 1081 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061562 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H]1C[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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] 1 hydrogens need rotated 492 conformations in input total number of sets (complete confs): 492 using faster count positions algorithm for large data unique positions, atoms: [50, 21, 50, 113, 157, 157, 157, 164, 164, 164, 164, 164, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 113, 113, 157, 164, 21, 21, 21, 1, 1, 3, 1, 1] 492 rigid atoms, others: [34, 35, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 632 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061562 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061562 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061562/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061562 Building REAL250005061563 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061563' /scratch/stefan/7916143/working/building/REAL250005061563 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061563 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061563/0 /scratch/stefan/7916143/working/building/REAL250005061563 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/693 `/scratch/stefan/7916143/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H]1C[C@H]1C) `REAL250005061563.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061563 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 71, 111, 111, 158, 158, 201, 201, 201, 201, 201, 71, 71, 71, 71, 25, 25, 5, 1, 111, 111, 111, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 741 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061563 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@@H]1C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 64, 138, 200, 200, 200, 201, 201, 201, 201, 201, 8, 26, 1, 8, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 138, 138, 200, 201, 26, 26, 26, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 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, 35, 36, 37]) total number of confs: 792 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061563 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061563 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061563/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061563 Building REAL250005061564 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061564' /scratch/stefan/7916143/working/building/REAL250005061564 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061564 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061564/0 /scratch/stefan/7916143/working/building/REAL250005061564 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/694 `/scratch/stefan/7916143/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061564.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061564 none CNC(=O)CC(=O)N(C)C(C)CNC(=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 191, 201, 112, 64, 112, 50, 64, 21, 48, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 191, 191, 64, 64, 64, 50, 50, 50, 50, 21, 21, 4, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 834 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061564 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061564 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061564/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061564 Building REAL250005061565 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061565' /scratch/stefan/7916143/working/building/REAL250005061565 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061565 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061565/0 /scratch/stefan/7916143/working/building/REAL250005061565 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/695 `/scratch/stefan/7916143/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC=CCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061565.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061565 none C=CC=CCC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 166, 101, 56, 101, 47, 56, 16, 47, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 166, 166, 56, 56, 56, 47, 47, 47, 47, 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: 806 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061565 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061565 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061565/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061565 Building REAL250005061566 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061566' /scratch/stefan/7916143/working/building/REAL250005061566 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061566 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061566/0 /scratch/stefan/7916143/working/building/REAL250005061566 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/696 `/scratch/stefan/7916143/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CCC(N)=O) `REAL250005061566.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061566 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)CCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 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 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [34, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 58, 58, 92, 92, 141, 175, 190, 190, 35, 35, 35, 35, 13, 13, 4, 1, 58, 58, 58, 141, 141, 175, 175, 190, 190] 190 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 833 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061566 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061566 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061566/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061566 Building REAL250005061567 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061567' /scratch/stefan/7916143/working/building/REAL250005061567 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061567 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061567/0 /scratch/stefan/7916143/working/building/REAL250005061567 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/697 `/scratch/stefan/7916143/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCC(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061567.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061567 none CC(O)CCC(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 175, 201, 169, 114, 64, 114, 47, 64, 17, 45, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 603, 176, 176, 169, 169, 64, 64, 64, 47, 47, 47, 47, 17, 17, 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: 1460 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061567 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061567 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061567/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061567 Building REAL250005061568 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061568' /scratch/stefan/7916143/working/building/REAL250005061568 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061568 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061568/0 /scratch/stefan/7916143/working/building/REAL250005061568 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/698 `/scratch/stefan/7916143/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061568.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061568 none C#CCC(C)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 173, 128, 173, 79, 128, 55, 79, 18, 52, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 173, 173, 173, 173, 79, 79, 79, 55, 55, 55, 55, 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: 877 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061568 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061568 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061568/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061568 Building REAL250005061569 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061569' /scratch/stefan/7916143/working/building/REAL250005061569 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061569 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061569/0 /scratch/stefan/7916143/working/building/REAL250005061569 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/699 `/scratch/stefan/7916143/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCO)C(=O)N(C)C(C)CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061569.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061569 none CC(CCO)C(=O)N(C)C(C)CNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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 543 conformations in input total number of sets (complete confs): 543 using faster count positions algorithm for large data unique positions, atoms: [158, 125, 158, 176, 181, 82, 125, 55, 82, 17, 51, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 181, 181, 181, 176, 543, 82, 82, 82, 55, 55, 55, 55, 17, 17, 4, 1] 543 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: 1336 number of broken/clashed sets: 197 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061569 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061569 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061569/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061569 Building REAL250005061570 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061570' /scratch/stefan/7916143/working/building/REAL250005061570 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061570 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061570/0 /scratch/stefan/7916143/working/building/REAL250005061570 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/700 `/scratch/stefan/7916143/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H](O)CF) `REAL250005061570.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061570 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)[C@H](O)CF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 7, 12, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 291 conformations in input total number of sets (complete confs): 291 using faster count positions algorithm for large data unique positions, atoms: [40, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 40, 63, 63, 80, 80, 95, 95, 95, 97, 40, 40, 40, 40, 17, 17, 4, 1, 63, 63, 63, 285, 97, 97] 291 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 684 number of broken/clashed sets: 153 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061570 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061570 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061570/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061570 Building REAL250005061571 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061571' /scratch/stefan/7916143/working/building/REAL250005061571 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061571 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061571/0 /scratch/stefan/7916143/working/building/REAL250005061571 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/701 `/scratch/stefan/7916143/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(O)CC1) `REAL250005061571.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061571 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 462 conformations in input total number of sets (complete confs): 462 using faster count positions algorithm for large data unique positions, atoms: [62, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 98, 98, 139, 139, 154, 154, 154, 65, 65, 65, 65, 23, 23, 4, 1, 98, 98, 98, 462, 154, 154, 154, 154] 462 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1029 number of broken/clashed sets: 121 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061571 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 462 conformations in input total number of sets (complete confs): 462 using faster count positions algorithm for large data unique positions, atoms: [52, 19, 52, 110, 154, 154, 154, 154, 154, 154, 154, 154, 7, 19, 1, 7, 1, 1, 1, 1, 52, 52, 52, 52, 110, 110, 154, 154, 19, 19, 19, 6, 1, 1, 1, 1] 462 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 618 number of broken/clashed sets: 121 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061571 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061571 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061571/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061571 Building REAL250005061572 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061572' /scratch/stefan/7916143/working/building/REAL250005061572 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061572 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061572/0 /scratch/stefan/7916143/working/building/REAL250005061572 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/702 `/scratch/stefan/7916143/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061572.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061572 none CC(CNC(=O)CC1CC1)N(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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 89, 23, 23, 3, 23, 1, 1, 1, 1, 152, 172, 172, 198, 198, 201, 201, 201, 201, 201, 152, 152, 152, 152, 89, 89, 23, 3, 3, 1, 1, 1, 1, 1, 172, 172, 172, 201] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37]) total number of confs: 833 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061572 none CC(CNC(=O)CC1CC1)N(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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 32, 54, 87, 87, 87, 162, 201, 201, 7, 21, 1, 7, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 54, 54, 87, 162, 162, 201, 201, 201, 201, 201, 21, 21, 21, 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: 866 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061572 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061572 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061572/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061572 Building REAL250005061573 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061573' /scratch/stefan/7916143/working/building/REAL250005061573 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061573 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061573/0 /scratch/stefan/7916143/working/building/REAL250005061573 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/703 `/scratch/stefan/7916143/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)(C)F)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061573.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061573 none CC(CNC(=O)C(C)(C)F)N(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.3', 'C.3', 'C.3', 'F', '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, 5, 5, 5, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 8, 10, 13, 18, 18, 18, 27, 27, 27, 6, 8, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 13, 13, 18, 27, 27, 27, 27, 27, 27, 8, 8, 8, 1] 27 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: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061573 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061573 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061573/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061573 Building REAL250005061574 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061574' /scratch/stefan/7916143/working/building/REAL250005061574 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061574 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061574/0 /scratch/stefan/7916143/working/building/REAL250005061574 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/704 `/scratch/stefan/7916143/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)(F)F)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061574.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061574 none CC(CNC(=O)C(C)(F)F)N(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.3', 'C.3', 'F', 'F', '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, 8, 1, 11, 5, 5, 15, 15, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 6, 6, 6, 6, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 15, 15, 15, 5, 5, 5, 1] 15 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: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061574 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061574 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061574/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061574 Building REAL250005061575 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061575' /scratch/stefan/7916143/working/building/REAL250005061575 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061575 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061575/0 /scratch/stefan/7916143/working/building/REAL250005061575 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/705 `/scratch/stefan/7916143/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061575.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061575 none COCC(=O)NCC(C)N(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 46, 46, 46, 25, 15, 13, 15, 7, 13, 1, 7, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 46, 25, 25, 15, 15, 15, 15, 13, 13, 13, 1] 82 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: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061575 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061575 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061575/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061575 Building REAL250005061576 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061576' /scratch/stefan/7916143/working/building/REAL250005061576 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061576 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061576/0 /scratch/stefan/7916143/working/building/REAL250005061576 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/706 `/scratch/stefan/7916143/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061576.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061576 none CCCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 180, 93, 93, 93, 58, 33, 20, 33, 7, 20, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 180, 180, 93, 58, 58, 33, 33, 33, 33, 20, 20, 20, 1] 201 rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 888 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061576 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061576 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061576/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061576 Building REAL250005061577 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061577' /scratch/stefan/7916143/working/building/REAL250005061577 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061577 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061577/0 /scratch/stefan/7916143/working/building/REAL250005061577 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/707 `/scratch/stefan/7916143/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=CO1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061577.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061577 none CC(CNC(=O)C1=CC=CO1)N(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', 'C.2', 'C.2', 'C.2', 'O.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, 8, 1, 11, 1, 1, 1, 1, 12, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [54, 23, 5, 5, 1, 5, 1, 1, 1, 1, 1, 54, 84, 84, 146, 146, 158, 158, 158, 158, 158, 54, 54, 54, 54, 22, 22, 5, 1, 1, 1, 84, 84, 84, 158] 158 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 531 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061577 none CC(CNC(=O)C1=CC=CO1)N(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', 'C.2', 'C.2', 'C.2', 'O.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, 8, 1, 11, 1, 1, 1, 1, 12, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [63, 30, 63, 116, 154, 154, 154, 158, 158, 158, 158, 11, 30, 1, 11, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 116, 116, 154, 158, 158, 158, 30, 30, 30, 1] 158 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: 606 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061577 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061577 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061577/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061577 Building REAL250005061578 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061578' /scratch/stefan/7916143/working/building/REAL250005061578 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061578 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061578/0 /scratch/stefan/7916143/working/building/REAL250005061578 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/708 `/scratch/stefan/7916143/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061578.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061578 none CC(=O)NCC(=O)NCC(C)N(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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 58, 58, 58, 37, 22, 14, 22, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 74, 58, 37, 37, 22, 22, 22, 22, 14, 14, 14, 1] 74 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: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061578 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061578 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061578/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061578 Building REAL250005061579 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061579' /scratch/stefan/7916143/working/building/REAL250005061579 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061579 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061579/0 /scratch/stefan/7916143/working/building/REAL250005061579 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/709 `/scratch/stefan/7916143/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061579.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061579 none CC(C)CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 100, 100, 100, 60, 39, 22, 39, 7, 22, 1, 7, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 153, 153, 153, 153, 153, 100, 60, 60, 39, 39, 39, 39, 22, 22, 22, 1] 153 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: 652 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061579 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061579 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061579/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061579 Building REAL250005061580 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061580' /scratch/stefan/7916143/working/building/REAL250005061580 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061580 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061580/0 /scratch/stefan/7916143/working/building/REAL250005061580 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/710 `/scratch/stefan/7916143/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC1C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061580.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061580 none CC(CNC(=O)C1CC1C)N(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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [80, 45, 11, 11, 1, 11, 1, 1, 1, 1, 80, 100, 100, 143, 143, 147, 147, 147, 147, 147, 80, 80, 80, 80, 45, 45, 11, 1, 1, 1, 1, 2, 2, 2, 100, 100, 100, 147] 147 rigid atoms, others: [4, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 565 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061580 none CC(CNC(=O)C1CC1C)N(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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 19, 36, 55, 86, 86, 86, 147, 147, 147, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 55, 55, 86, 147, 147, 147, 147, 147, 147, 147, 19, 19, 19, 1] 147 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: 529 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061580 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061580 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061580/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061580 Building REAL250005061581 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061581' /scratch/stefan/7916143/working/building/REAL250005061581 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061581 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061581/0 /scratch/stefan/7916143/working/building/REAL250005061581 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/711 `/scratch/stefan/7916143/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061581.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061581 none CCOCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 64, 64, 64, 40, 23, 15, 23, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80, 80, 64, 40, 40, 23, 23, 23, 23, 15, 15, 15, 1] 80 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: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061581 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061581 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061581/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061581 Building REAL250005061582 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061582' /scratch/stefan/7916143/working/building/REAL250005061582 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061582 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061582/0 /scratch/stefan/7916143/working/building/REAL250005061582 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/712 `/scratch/stefan/7916143/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061582.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061582 none CC(C)=CC(=O)NCC(C)N(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 86, 86, 86, 53, 35, 19, 35, 9, 19, 1, 9, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 116, 116, 86, 53, 53, 35, 35, 35, 35, 19, 19, 19, 1] 116 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 442 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061582 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061582 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061582/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061582 Building REAL250005061583 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061583' /scratch/stefan/7916143/working/building/REAL250005061583 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061583 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061583/0 /scratch/stefan/7916143/working/building/REAL250005061583 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/713 `/scratch/stefan/7916143/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCCO1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061583.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061583 none CC(CNC(=O)C1CCCO1)N(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.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 5, 12, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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, 7, 7] 0 hydrogens 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, 41, 10, 10, 1, 10, 1, 1, 1, 1, 1, 94, 127, 127, 189, 189, 201, 201, 201, 201, 201, 94, 94, 94, 94, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 201] 201 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 725 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061583 none CC(CNC(=O)C1CCCO1)N(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.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 5, 12, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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, 7, 7] 0 hydrogens 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, 28, 57, 109, 182, 182, 182, 201, 201, 201, 201, 10, 28, 1, 10, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 109, 109, 182, 201, 201, 201, 201, 201, 201, 201, 28, 28, 28, 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: 743 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061583 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061583 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061583/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061583 Building REAL250005061584 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061584' /scratch/stefan/7916143/working/building/REAL250005061584 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061584 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061584/0 /scratch/stefan/7916143/working/building/REAL250005061584 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/714 `/scratch/stefan/7916143/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061584.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061584 none CSCC(=O)NCC(C)N(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 75, 45, 45, 45, 28, 17, 14, 17, 7, 14, 1, 7, 1, 1, 1, 1, 1, 1, 91, 91, 91, 75, 75, 45, 28, 28, 17, 17, 17, 17, 14, 14, 14, 1] 91 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061584 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061584 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061584/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061584 Building REAL250005061585 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061585' /scratch/stefan/7916143/working/building/REAL250005061585 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061585 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061585/0 /scratch/stefan/7916143/working/building/REAL250005061585 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/715 `/scratch/stefan/7916143/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061585.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061585 none CC(C)CCC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 51, 48, 18, 18, 18, 14, 11, 11, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 48, 48, 18, 14, 14, 11, 11, 11, 11, 11, 11, 11, 1] 51 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: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061585 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061585 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061585/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061585 Building REAL250005061586 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061586' /scratch/stefan/7916143/working/building/REAL250005061586 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061586 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061586/0 /scratch/stefan/7916143/working/building/REAL250005061586 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/716 `/scratch/stefan/7916143/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=CN1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061586.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061586 none CC(CNC(=O)C1=CC=CN1)N(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', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 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: [38, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 38, 54, 54, 85, 85, 95, 95, 95, 95, 95, 38, 38, 38, 38, 19, 19, 5, 1, 1, 1, 1, 54, 54, 54, 95] 95 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061586 none CC(CNC(=O)C1=CC=CN1)N(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', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 1, 1, 1, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 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: [47, 23, 47, 71, 93, 93, 93, 95, 95, 95, 95, 10, 23, 1, 10, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 71, 71, 93, 95, 95, 95, 95, 23, 23, 23, 1] 95 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: 374 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061586 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061586 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061586/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061586 Building REAL250005061587 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061587' /scratch/stefan/7916143/working/building/REAL250005061587 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061587 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061587/0 /scratch/stefan/7916143/working/building/REAL250005061587 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/717 `/scratch/stefan/7916143/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=COC=C1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061587.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061587 none CC(CNC(=O)C1=COC=C1)N(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', 'C.2', 'O.3', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 12, 1, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 32, 39, 39, 54, 54, 56, 56, 56, 56, 56, 32, 32, 32, 32, 21, 21, 5, 1, 1, 1, 39, 39, 39, 56] 56 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061587 none CC(CNC(=O)C1=COC=C1)N(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', 'C.2', 'O.3', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 12, 1, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 15, 21, 26, 39, 39, 39, 56, 56, 56, 56, 7, 15, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 26, 26, 39, 56, 56, 56, 15, 15, 15, 1] 56 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: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061587 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061587 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061587/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061587 Building REAL250005061588 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061588' /scratch/stefan/7916143/working/building/REAL250005061588 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061588 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061588/0 /scratch/stefan/7916143/working/building/REAL250005061588 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/718 `/scratch/stefan/7916143/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061588.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061588 none CCCCCC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 45, 18, 18, 18, 14, 13, 13, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 48, 45, 45, 18, 14, 14, 13, 13, 13, 13, 13, 13, 13, 1] 48 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: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061588 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061588 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061588/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061588 Building REAL250005061589 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061589' /scratch/stefan/7916143/working/building/REAL250005061589 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061589 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061589/0 /scratch/stefan/7916143/working/building/REAL250005061589 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/719 `/scratch/stefan/7916143/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC(C)(C)C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061589.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061589 none CC(CNC(=O)CC(C)(C)C)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 21, 39, 59, 92, 92, 92, 112, 113, 113, 113, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 59, 59, 92, 112, 112, 113, 113, 113, 113, 113, 113, 113, 113, 113, 21, 21, 21, 1] 113 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: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061589 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061589 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061589/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061589 Building REAL250005061590 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061590' /scratch/stefan/7916143/working/building/REAL250005061590 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061590 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061590/0 /scratch/stefan/7916143/working/building/REAL250005061590 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/720 `/scratch/stefan/7916143/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061590.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061590 none CCCCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 46, 18, 18, 18, 14, 12, 12, 12, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 46, 46, 18, 14, 14, 12, 12, 12, 12, 12, 12, 12, 1] 49 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061590 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061590 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061590/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061590 Building REAL250005061591 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061591' /scratch/stefan/7916143/working/building/REAL250005061591 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061591 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061591/0 /scratch/stefan/7916143/working/building/REAL250005061591 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/721 `/scratch/stefan/7916143/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061591.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061591 none CC(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 106, 164, 106, 106, 74, 46, 25, 46, 8, 25, 1, 8, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 164, 164, 106, 74, 74, 46, 46, 46, 46, 25, 25, 25, 1] 164 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: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061591 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061591 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061591/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061591 Building REAL250005061592 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061592' /scratch/stefan/7916143/working/building/REAL250005061592 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061592 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061592/0 /scratch/stefan/7916143/working/building/REAL250005061592 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/722 `/scratch/stefan/7916143/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061592.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061592 none CCC(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 193, 108, 193, 108, 108, 60, 37, 20, 37, 7, 20, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 193, 193, 193, 108, 60, 60, 37, 37, 37, 37, 20, 20, 20, 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: 851 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061592 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061592 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061592/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061592 Building REAL250005061593 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061593' /scratch/stefan/7916143/working/building/REAL250005061593 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061593 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061593/0 /scratch/stefan/7916143/working/building/REAL250005061593 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/723 `/scratch/stefan/7916143/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061593.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061593 none CCC(CC)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [154, 139, 98, 139, 158, 98, 98, 56, 36, 22, 36, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 139, 158, 158, 158, 158, 158, 98, 56, 56, 36, 36, 36, 36, 22, 22, 22, 1] 160 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: 810 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061593 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061593 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061593/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061593 Building REAL250005061594 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061594' /scratch/stefan/7916143/working/building/REAL250005061594 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061594 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061594/0 /scratch/stefan/7916143/working/building/REAL250005061594 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/724 `/scratch/stefan/7916143/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=NN1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061594.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061594 none CC(CNC(=O)C1=CC=NN1)N(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', 'C.2', 'C.2', 'N.2', 'N.pl3', '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, 8, 1, 11, 1, 1, 1, 8, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 21, 27, 27, 39, 39, 41, 41, 41, 41, 41, 21, 21, 21, 21, 12, 12, 4, 1, 1, 1, 27, 27, 27, 41] 41 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061594 none CC(CNC(=O)C1=CC=NN1)N(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', 'C.2', 'C.2', 'N.2', 'N.pl3', '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, 8, 1, 11, 1, 1, 1, 8, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [25, 16, 25, 30, 39, 39, 39, 41, 41, 41, 41, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 30, 30, 39, 41, 41, 41, 16, 16, 16, 1] 41 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: 152 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061594 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061594 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061594/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061594 Building REAL250005061595 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061595' /scratch/stefan/7916143/working/building/REAL250005061595 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061595 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061595/0 /scratch/stefan/7916143/working/building/REAL250005061595 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/725 `/scratch/stefan/7916143/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061595.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061595 none CCOC(C)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 62, 83, 62, 62, 40, 23, 16, 23, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 83, 83, 62, 40, 40, 23, 23, 23, 23, 16, 16, 16, 1] 83 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: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061595 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061595 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061595/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061595 Building REAL250005061596 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061596' /scratch/stefan/7916143/working/building/REAL250005061596 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061596 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061596/0 /scratch/stefan/7916143/working/building/REAL250005061596 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/726 `/scratch/stefan/7916143/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CNN=C1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061596.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061596 none CC(CNC(=O)C1=CNN=C1)N(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', 'C.2', 'N.pl3', 'N.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 8, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 20, 26, 26, 35, 35, 35, 35, 35, 35, 35, 20, 20, 20, 20, 11, 11, 3, 1, 1, 1, 26, 26, 26, 35] 35 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061596 none CC(CNC(=O)C1=CNN=C1)N(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', 'C.2', 'N.pl3', 'N.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 8, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 22, 28, 35, 35, 35, 35, 35, 35, 35, 7, 15, 1, 7, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 28, 28, 35, 35, 35, 35, 15, 15, 15, 1] 35 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: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061596 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061596 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061596/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061596 Building REAL250005061597 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061597' /scratch/stefan/7916143/working/building/REAL250005061597 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061597 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061597/0 /scratch/stefan/7916143/working/building/REAL250005061597 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/727 `/scratch/stefan/7916143/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061597.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061597 none COCCCC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 69, 69, 24, 24, 24, 22, 13, 11, 13, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 76, 76, 76, 72, 73, 76, 76, 69, 69, 24, 22, 22, 13, 13, 13, 13, 11, 11, 11, 1] 76 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: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061597 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061597 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061597/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061597 Building REAL250005061598 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061598' /scratch/stefan/7916143/working/building/REAL250005061598 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061598 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061598/0 /scratch/stefan/7916143/working/building/REAL250005061598 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/728 `/scratch/stefan/7916143/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=NOC=C1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061598.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061598 none CC(CNC(=O)C1=NOC=C1)N(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', 'N.2', 'O.3', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 8, 12, 1, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 63, 105, 105, 180, 180, 201, 201, 201, 201, 201, 63, 63, 63, 63, 24, 24, 6, 1, 1, 105, 105, 105, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 650 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061598 none CC(CNC(=O)C1=NOC=C1)N(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', 'N.2', 'O.3', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 8, 12, 1, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 75, 145, 199, 199, 199, 201, 201, 201, 201, 11, 36, 1, 11, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 145, 145, 199, 201, 201, 36, 36, 36, 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: 796 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061598 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061598 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061598/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061598 Building REAL250005061599 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061599' /scratch/stefan/7916143/working/building/REAL250005061599 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061599 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061599/0 /scratch/stefan/7916143/working/building/REAL250005061599 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/729 `/scratch/stefan/7916143/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061599.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061599 none CCC=C(C)C(=O)NCC(C)N(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', '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, 1, 5, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 24, 24, 15, 24, 15, 15, 12, 11, 9, 11, 6, 9, 1, 6, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 24, 24, 24, 24, 15, 12, 12, 11, 11, 11, 11, 9, 9, 9, 1] 25 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: 89 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061599 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061599 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061599/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061599 Building REAL250005061600 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061600' /scratch/stefan/7916143/working/building/REAL250005061600 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061600 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061600/0 /scratch/stefan/7916143/working/building/REAL250005061600 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/730 `/scratch/stefan/7916143/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061600.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061600 none COC(C)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 38, 55, 38, 38, 26, 17, 15, 17, 7, 15, 1, 7, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 38, 26, 26, 17, 17, 17, 17, 15, 15, 15, 1] 55 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: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061600 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061600 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061600/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061600 Building REAL250005061601 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061601' /scratch/stefan/7916143/working/building/REAL250005061601 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061601 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061601/0 /scratch/stefan/7916143/working/building/REAL250005061601 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/731 `/scratch/stefan/7916143/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061601.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061601 none CC(C)OCC(=O)NCC(C)N(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', '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, 12, 5, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 170, 201, 114, 101, 101, 101, 45, 28, 17, 28, 9, 17, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 114, 114, 101, 45, 45, 28, 28, 28, 28, 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: 710 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061601 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061601 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061601/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061601 Building REAL250005061602 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061602' /scratch/stefan/7916143/working/building/REAL250005061602 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061602 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061602/0 /scratch/stefan/7916143/working/building/REAL250005061602 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/732 `/scratch/stefan/7916143/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061602.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061602 none CCCOCC(=O)NCC(C)N(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', '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, 12, 5, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 130, 77, 56, 56, 56, 24, 19, 13, 19, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 176, 176, 77, 77, 56, 24, 24, 19, 19, 19, 19, 13, 13, 13, 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: 781 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061602 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061602 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061602/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061602 Building REAL250005061603 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061603' /scratch/stefan/7916143/working/building/REAL250005061603 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061603 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061603/0 /scratch/stefan/7916143/working/building/REAL250005061603 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/733 `/scratch/stefan/7916143/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCOC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061603.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061603 none CC(CNC(=O)C1CCOC1)N(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.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 12, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [67, 37, 8, 8, 1, 8, 1, 1, 1, 1, 1, 67, 81, 81, 131, 131, 149, 149, 149, 149, 149, 67, 67, 67, 67, 37, 37, 8, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 149] 149 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 525 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061603 none CC(CNC(=O)C1CCOC1)N(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.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 12, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [40, 19, 40, 65, 105, 105, 105, 149, 149, 149, 149, 9, 19, 1, 9, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 65, 65, 105, 149, 149, 149, 149, 149, 149, 149, 19, 19, 19, 1] 149 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: 552 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061603 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061603 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061603/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061603 Building REAL250005061604 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061604' /scratch/stefan/7916143/working/building/REAL250005061604 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061604 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061604/0 /scratch/stefan/7916143/working/building/REAL250005061604 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/734 `/scratch/stefan/7916143/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061604.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061604 none CCC(OC)C(=O)NCC(C)N(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', '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, 12, 5, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [89, 89, 46, 89, 93, 46, 46, 28, 17, 15, 17, 7, 15, 1, 7, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 89, 93, 93, 93, 46, 28, 28, 17, 17, 17, 17, 15, 15, 15, 1] 97 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 459 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061604 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061604 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061604/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061604 Building REAL250005061605 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061605' /scratch/stefan/7916143/working/building/REAL250005061605 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061605 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061605/0 /scratch/stefan/7916143/working/building/REAL250005061605 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/735 `/scratch/stefan/7916143/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061605.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061605 none COC(C)CC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 14, 12, 12, 12, 9, 7, 6, 7, 5, 6, 1, 5, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 13, 13, 12, 9, 9, 7, 7, 7, 7, 6, 6, 6, 1] 14 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061605 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061605 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061605/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061605 Building REAL250005061606 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061606' /scratch/stefan/7916143/working/building/REAL250005061606 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061606 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061606/0 /scratch/stefan/7916143/working/building/REAL250005061606 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/736 `/scratch/stefan/7916143/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061606.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061606 none C=CCCC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 14, 14, 14, 13, 9, 8, 9, 6, 8, 1, 6, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 14, 13, 13, 9, 9, 9, 9, 8, 8, 8, 1] 31 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061606 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061606 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061606/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061606 Building REAL250005061607 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061607' /scratch/stefan/7916143/working/building/REAL250005061607 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061607 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061607/0 /scratch/stefan/7916143/working/building/REAL250005061607 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/737 `/scratch/stefan/7916143/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061607.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061607 none CCOCCC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 20, 20, 20, 19, 10, 9, 10, 6, 9, 1, 6, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 20, 19, 19, 10, 10, 10, 10, 9, 9, 9, 1] 37 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061607 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061607 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061607/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061607 Building REAL250005061608 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061608' /scratch/stefan/7916143/working/building/REAL250005061608 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061608 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061608/0 /scratch/stefan/7916143/working/building/REAL250005061608 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/738 `/scratch/stefan/7916143/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061608.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061608 none COCC(C)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 22, 29, 22, 22, 18, 11, 11, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 22, 18, 18, 11, 11, 11, 11, 11, 11, 11, 1] 29 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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061608 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061608 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061608/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061608 Building REAL250005061609 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061609' /scratch/stefan/7916143/working/building/REAL250005061609 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061609 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061609/0 /scratch/stefan/7916143/working/building/REAL250005061609 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/739 `/scratch/stefan/7916143/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061609.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061609 none C=CCOCC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 133, 73, 53, 53, 53, 22, 18, 12, 18, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 73, 73, 53, 22, 22, 18, 18, 18, 18, 12, 12, 12, 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: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061609 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061609 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061609/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061609 Building REAL250005061610 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061610' /scratch/stefan/7916143/working/building/REAL250005061610 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061610 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061610/0 /scratch/stefan/7916143/working/building/REAL250005061610 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/740 `/scratch/stefan/7916143/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=COC=N1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061610.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061610 none CC(CNC(=O)C1=COC=N1)N(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', 'C.2', 'O.3', 'C.2', 'N.2', '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, 5, 8, 1, 11, 1, 1, 12, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [54, 18, 5, 5, 1, 5, 1, 1, 1, 1, 1, 55, 92, 92, 164, 164, 179, 179, 179, 179, 179, 55, 55, 55, 55, 18, 18, 5, 1, 1, 92, 92, 92, 179] 179 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 582 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061610 none CC(CNC(=O)C1=COC=N1)N(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', 'C.2', 'O.3', 'C.2', 'N.2', '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, 5, 8, 1, 11, 1, 1, 12, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [70, 32, 70, 128, 179, 179, 179, 179, 179, 179, 179, 10, 32, 1, 10, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 128, 128, 179, 179, 179, 32, 32, 32, 1] 179 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: 705 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061610 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061610 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061610/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061610 Building REAL250005061611 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061611' /scratch/stefan/7916143/working/building/REAL250005061611 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061611 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061611/0 /scratch/stefan/7916143/working/building/REAL250005061611 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/741 `/scratch/stefan/7916143/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061611.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061611 none CC(C#N)C(=O)NCC(C)N(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 36, 50, 50, 36, 36, 28, 17, 14, 17, 7, 14, 1, 7, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 36, 28, 28, 17, 17, 17, 17, 14, 14, 14, 1] 50 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: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061611 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061611 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061611/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061611 Building REAL250005061612 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061612' /scratch/stefan/7916143/working/building/REAL250005061612 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061612 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061612/0 /scratch/stefan/7916143/working/building/REAL250005061612 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/742 `/scratch/stefan/7916143/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061612.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061612 none CCCC(C)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 41, 21, 41, 21, 21, 14, 13, 11, 13, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 41, 41, 41, 41, 21, 14, 14, 13, 13, 13, 13, 11, 11, 11, 1] 43 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: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061612 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061612 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061612/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061612 Building REAL250005061613 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061613' /scratch/stefan/7916143/working/building/REAL250005061613 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061613 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061613/0 /scratch/stefan/7916143/working/building/REAL250005061613 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/743 `/scratch/stefan/7916143/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCC1CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061613.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061613 none CC(CNC(=O)CCC1CC1)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 117, 35, 35, 7, 35, 3, 1, 1, 1, 1, 170, 176, 176, 200, 200, 201, 201, 201, 201, 201, 170, 170, 170, 170, 117, 117, 35, 7, 7, 3, 3, 1, 1, 1, 1, 1, 176, 176, 176, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40]) total number of confs: 850 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061613 none CC(CNC(=O)CCC1CC1)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 17, 31, 56, 56, 56, 147, 163, 201, 201, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 31, 31, 56, 147, 147, 169, 169, 201, 201, 201, 201, 201, 13, 13, 13, 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: 872 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061613 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061613 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061613/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061613 Building REAL250005061614 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061614' /scratch/stefan/7916143/working/building/REAL250005061614 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061614 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061614/0 /scratch/stefan/7916143/working/building/REAL250005061614 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/744 `/scratch/stefan/7916143/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC=CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061614.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061614 none CC(CNC(=O)C1CC=CC1)N(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.3', 'C.3', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [67, 43, 9, 9, 1, 9, 1, 1, 1, 1, 1, 67, 79, 79, 102, 102, 106, 106, 106, 106, 106, 67, 67, 67, 67, 43, 43, 9, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 106] 106 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061614 none CC(CNC(=O)C1CC=CC1)N(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.3', 'C.3', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 15, 22, 37, 62, 62, 62, 106, 106, 106, 106, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 37, 37, 62, 106, 106, 106, 106, 106, 106, 106, 15, 15, 15, 1] 106 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: 369 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061614 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061614 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061614/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061614 Building REAL250005061615 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061615' /scratch/stefan/7916143/working/building/REAL250005061615 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061615 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061615/0 /scratch/stefan/7916143/working/building/REAL250005061615 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/745 `/scratch/stefan/7916143/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1CCC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061615.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061615 none CC(CNC(=O)CC1CCC1)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 103, 37, 37, 7, 37, 1, 1, 1, 1, 1, 154, 169, 169, 198, 198, 201, 201, 201, 201, 201, 154, 154, 154, 154, 103, 103, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 169, 169, 169, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40]) total number of confs: 796 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061615 none CC(CNC(=O)CC1CCC1)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 27, 51, 93, 93, 93, 165, 201, 201, 201, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 51, 51, 93, 165, 165, 201, 201, 201, 201, 201, 201, 201, 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: 857 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061615 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061615 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061615/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061615 Building REAL250005061616 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061616' /scratch/stefan/7916143/working/building/REAL250005061616 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061616 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061616/0 /scratch/stefan/7916143/working/building/REAL250005061616 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/746 `/scratch/stefan/7916143/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)C1CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061616.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061616 none CC(CNC(=O)C(C)C1CC1)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [101, 63, 21, 21, 4, 21, 1, 4, 1, 1, 1, 101, 118, 118, 139, 139, 143, 143, 143, 143, 143, 101, 101, 101, 101, 63, 63, 21, 4, 4, 4, 4, 1, 1, 1, 1, 1, 118, 118, 118, 143] 143 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40]) total number of confs: 570 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061616 none CC(CNC(=O)C(C)C1CC1)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 23, 33, 52, 75, 75, 75, 143, 143, 143, 143, 7, 23, 1, 7, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 52, 52, 75, 143, 143, 143, 143, 143, 143, 143, 143, 143, 23, 23, 23, 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: 588 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061616 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061616 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061616/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061616 Building REAL250005061617 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061617' /scratch/stefan/7916143/working/building/REAL250005061617 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061617 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061617/0 /scratch/stefan/7916143/working/building/REAL250005061617 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/747 `/scratch/stefan/7916143/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061617.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061617 none CC=C(C)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 110, 154, 110, 110, 74, 44, 20, 44, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 154, 154, 154, 110, 74, 74, 44, 44, 44, 44, 20, 20, 20, 1] 154 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: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061617 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061617 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061617/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061617 Building REAL250005061618 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061618' /scratch/stefan/7916143/working/building/REAL250005061618 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061618 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061618/0 /scratch/stefan/7916143/working/building/REAL250005061618 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/748 `/scratch/stefan/7916143/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC(C)C1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061618.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061618 none CC(CNC(=O)C1CC(C)C1)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [77, 41, 10, 10, 1, 10, 1, 1, 1, 1, 1, 77, 103, 103, 135, 135, 141, 141, 141, 141, 141, 77, 77, 77, 77, 41, 41, 10, 1, 1, 1, 1, 2, 2, 2, 1, 1, 103, 103, 103, 141] 141 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 36, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 547 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061618 none CC(CNC(=O)C1CC(C)C1)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 19, 34, 52, 85, 85, 85, 141, 141, 141, 141, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 52, 52, 85, 141, 141, 141, 141, 141, 141, 141, 141, 141, 19, 19, 19, 1] 141 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: 510 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061618 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061618 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061618/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061618 Building REAL250005061619 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061619' /scratch/stefan/7916143/working/building/REAL250005061619 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061619 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061619/0 /scratch/stefan/7916143/working/building/REAL250005061619 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/749 `/scratch/stefan/7916143/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=C1CCC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061619.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061619 none CC(CNC(=O)C=C1CCC1)N(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', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [62, 34, 7, 7, 1, 7, 1, 1, 1, 1, 1, 62, 77, 77, 112, 112, 116, 116, 116, 116, 116, 62, 62, 62, 62, 34, 34, 7, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 116] 116 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061619 none CC(CNC(=O)C=C1CCC1)N(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', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 17, 30, 49, 78, 78, 78, 116, 116, 116, 116, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 49, 49, 78, 116, 116, 116, 116, 116, 116, 116, 17, 17, 17, 1] 116 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: 424 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061619 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061619 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061619/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061619 Building REAL250005061620 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061620' /scratch/stefan/7916143/working/building/REAL250005061620 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061620 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061620/0 /scratch/stefan/7916143/working/building/REAL250005061620 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/750 `/scratch/stefan/7916143/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061620.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061620 none CC(C)=C(F)C(=O)NCC(C)N(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', '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, 5, 1, 15, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 75, 94, 75, 75, 47, 32, 17, 32, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 94, 75, 47, 47, 32, 32, 32, 32, 17, 17, 17, 1] 94 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: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061620 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061620 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061620/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061620 Building REAL250005061621 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061621' /scratch/stefan/7916143/working/building/REAL250005061621 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061621 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061621/0 /scratch/stefan/7916143/working/building/REAL250005061621 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/751 `/scratch/stefan/7916143/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCCC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061621.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061621 none CC(CNC(=O)C1=CCCC1)N(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', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 38, 47, 47, 57, 57, 58, 58, 58, 58, 58, 38, 38, 38, 38, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 58] 58 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061621 none CC(CNC(=O)C1=CCCC1)N(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', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 19, 31, 48, 57, 57, 57, 58, 58, 58, 58, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 48, 48, 57, 58, 58, 58, 58, 58, 58, 58, 19, 19, 19, 1] 58 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: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061621 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061621 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061621/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061621 Building REAL250005061622 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061622' /scratch/stefan/7916143/working/building/REAL250005061622 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061622 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061622/0 /scratch/stefan/7916143/working/building/REAL250005061622 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/752 `/scratch/stefan/7916143/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC1(C)C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061622.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061622 none CC(CNC(=O)C1CC1(C)C)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [61, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 61, 78, 78, 117, 117, 124, 124, 124, 124, 124, 61, 61, 61, 61, 27, 27, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 78, 78, 78, 124] 124 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061622 none CC(CNC(=O)C1CC1(C)C)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 20, 37, 60, 95, 95, 95, 124, 124, 124, 124, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 60, 60, 95, 124, 124, 124, 124, 124, 124, 124, 124, 124, 20, 20, 20, 1] 124 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: 473 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061622 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061622 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061622/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061622 Building REAL250005061623 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061623' /scratch/stefan/7916143/working/building/REAL250005061623 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061623 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061623/0 /scratch/stefan/7916143/working/building/REAL250005061623 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/753 `/scratch/stefan/7916143/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H]1CC1(C)C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061623.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061623 none CC(CNC(=O)[C@H]1CC1(C)C)N(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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [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, 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: [52, 24, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 52, 65, 65, 90, 90, 97, 97, 97, 97, 97, 52, 52, 52, 52, 24, 24, 5, 1, 1, 2, 2, 2, 2, 2, 2, 65, 65, 65, 97] 97 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061623 none CC(CNC(=O)[C@H]1CC1(C)C)N(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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [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, 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: [33, 18, 33, 47, 75, 75, 75, 97, 97, 97, 97, 97, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 47, 47, 75, 97, 97, 97, 97, 97, 97, 97, 97, 18, 18, 18, 1] 97 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: 364 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061623 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061623 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061623/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061623 Building REAL250005061624 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061624' /scratch/stefan/7916143/working/building/REAL250005061624 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061624 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061624/0 /scratch/stefan/7916143/working/building/REAL250005061624 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/754 `/scratch/stefan/7916143/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1CCCO1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061624.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061624 none CC(CNC(=O)[C@@H]1CCCO1)N(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.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 5, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 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, 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: [89, 44, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 89, 116, 116, 159, 159, 171, 171, 171, 171, 171, 89, 89, 89, 89, 44, 44, 11, 1, 1, 1, 1, 1, 1, 116, 116, 116, 171] 171 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38]) total number of confs: 636 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061624 none CC(CNC(=O)[C@@H]1CCCO1)N(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.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 5, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 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, 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: [49, 25, 49, 83, 147, 147, 147, 171, 171, 171, 171, 171, 11, 25, 1, 11, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 83, 83, 147, 171, 171, 171, 171, 171, 171, 25, 25, 25, 1] 171 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: 639 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061624 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061624 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061624/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061624 Building REAL250005061625 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061625' /scratch/stefan/7916143/working/building/REAL250005061625 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061625 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061625/0 /scratch/stefan/7916143/working/building/REAL250005061625 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/755 `/scratch/stefan/7916143/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061625.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061625 none CCC(C)CC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 52, 55, 15, 15, 15, 14, 13, 11, 13, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 55, 52, 52, 15, 14, 14, 13, 13, 13, 13, 11, 11, 11, 1] 55 rigid atoms, others: [42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061625 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061625 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061625/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061625 Building REAL250005061626 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061626' /scratch/stefan/7916143/working/building/REAL250005061626 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061626 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061626/0 /scratch/stefan/7916143/working/building/REAL250005061626 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/756 `/scratch/stefan/7916143/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061626.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061626 none C#CCCCC(=O)NCC(C)N(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', '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, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 39, 47, 17, 17, 17, 11, 11, 9, 11, 6, 9, 1, 6, 1, 1, 1, 1, 1, 1, 54, 49, 48, 50, 50, 47, 47, 17, 11, 11, 11, 11, 11, 11, 9, 9, 9, 1] 54 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: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061626 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061626 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061626/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061626 Building REAL250005061627 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061627' /scratch/stefan/7916143/working/building/REAL250005061627 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061627 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061627/0 /scratch/stefan/7916143/working/building/REAL250005061627 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/757 `/scratch/stefan/7916143/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC(C)(C)O)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061627.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061627 none CC(CNC(=O)CC(C)(C)O)N(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.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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, 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: [26, 18, 26, 42, 60, 60, 60, 75, 81, 81, 81, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 42, 42, 60, 75, 75, 81, 81, 81, 81, 81, 81, 243, 18, 18, 18, 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: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061627 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061627 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061627/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061627 Building REAL250005061628 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061628' /scratch/stefan/7916143/working/building/REAL250005061628 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061628 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061628/0 /scratch/stefan/7916143/working/building/REAL250005061628 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/758 `/scratch/stefan/7916143/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061628.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061628 none CC(C)[C@@H](O)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [77, 74, 78, 46, 74, 74, 46, 46, 24, 14, 12, 14, 7, 12, 1, 7, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 78, 222, 46, 24, 24, 14, 14, 14, 14, 12, 12, 12, 1] 234 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: 547 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061628 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061628 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061628/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061628 Building REAL250005061629 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061629' /scratch/stefan/7916143/working/building/REAL250005061629 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061629 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061629/0 /scratch/stefan/7916143/working/building/REAL250005061629 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/759 `/scratch/stefan/7916143/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061629.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061629 none CCC(C)=CC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 47, 47, 47, 34, 34, 34, 21, 17, 12, 17, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 47, 47, 47, 47, 34, 21, 21, 17, 17, 17, 17, 12, 12, 12, 1] 74 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: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061629 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061629 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061629/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061629 Building REAL250005061630 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061630' /scratch/stefan/7916143/working/building/REAL250005061630 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061630 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061630/0 /scratch/stefan/7916143/working/building/REAL250005061630 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/760 `/scratch/stefan/7916143/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C#CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061630.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061630 none CC(C)C#CC(=O)NCC(C)N(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', '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, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 65, 65, 51, 35, 19, 35, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 51, 51, 35, 35, 35, 35, 19, 19, 19, 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: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061630 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061630 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061630/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061630 Building REAL250005061631 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061631' /scratch/stefan/7916143/working/building/REAL250005061631 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061631 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061631/0 /scratch/stefan/7916143/working/building/REAL250005061631 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/761 `/scratch/stefan/7916143/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C#CC1CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061631.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061631 none CC(CNC(=O)C#CC1CC1)N(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.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 35, 35, 55, 55, 60, 60, 60, 60, 60, 23, 23, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 35, 35, 35, 60] 60 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061631 none CC(CNC(=O)C#CC1CC1)N(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.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 19, 34, 48, 60, 60, 60, 60, 60, 60, 60, 9, 19, 1, 9, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 48, 48, 60, 60, 60, 60, 60, 60, 19, 19, 19, 1] 60 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: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061631 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061631 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061631/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061631 Building REAL250005061632 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061632' /scratch/stefan/7916143/working/building/REAL250005061632 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061632 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061632/0 /scratch/stefan/7916143/working/building/REAL250005061632 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/762 `/scratch/stefan/7916143/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061632.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061632 none CCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 98, 98, 98, 71, 42, 24, 42, 8, 24, 1, 8, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 98, 71, 71, 42, 42, 42, 42, 24, 24, 24, 1] 135 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: 614 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061632 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061632 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061632/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061632 Building REAL250005061633 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061633' /scratch/stefan/7916143/working/building/REAL250005061633 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061633 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061633/0 /scratch/stefan/7916143/working/building/REAL250005061633 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/763 `/scratch/stefan/7916143/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061633.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061633 none COCCC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 37, 23, 23, 23, 22, 13, 12, 13, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 37, 37, 23, 22, 22, 13, 13, 13, 13, 12, 12, 12, 1] 40 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: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061633 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061633 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061633/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061633 Building REAL250005061634 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061634' /scratch/stefan/7916143/working/building/REAL250005061634 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061634 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061634/0 /scratch/stefan/7916143/working/building/REAL250005061634 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/764 `/scratch/stefan/7916143/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061634.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061634 none CC(CNC(=O)C1CC1)N(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.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 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, 7] dock color type numbers: [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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [100, 45, 11, 11, 1, 11, 1, 1, 1, 100, 135, 135, 179, 179, 187, 187, 187, 187, 187, 100, 100, 100, 100, 45, 45, 11, 1, 1, 1, 1, 1, 135, 135, 135, 187] 187 rigid atoms, others: [4, 6, 7, 8, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 702 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061634 none CC(CNC(=O)C1CC1)N(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.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 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, 7] dock color type numbers: [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 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [44, 24, 44, 75, 102, 102, 102, 186, 186, 8, 24, 1, 8, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 75, 75, 102, 186, 186, 186, 186, 186, 24, 24, 24, 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: 670 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061634 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061634 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061634/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061634 Building REAL250005061635 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061635' /scratch/stefan/7916143/working/building/REAL250005061635 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061635 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061635/0 /scratch/stefan/7916143/working/building/REAL250005061635 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/765 `/scratch/stefan/7916143/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061635.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061635 none CC(CNC(=O)C1CCC1)N(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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [76, 42, 11, 11, 1, 11, 1, 1, 1, 1, 76, 98, 98, 141, 141, 147, 147, 147, 147, 147, 76, 76, 76, 76, 42, 42, 11, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 147] 147 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37]) total number of confs: 550 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061635 none CC(CNC(=O)C1CCC1)N(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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 19, 36, 53, 82, 82, 82, 147, 147, 147, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 53, 53, 82, 147, 147, 147, 147, 147, 147, 147, 19, 19, 19, 1] 147 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: 515 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061635 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061635 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061635/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061635 Building REAL250005061636 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061636' /scratch/stefan/7916143/working/building/REAL250005061636 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061636 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061636/0 /scratch/stefan/7916143/working/building/REAL250005061636 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/766 `/scratch/stefan/7916143/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCCC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061636.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061636 none CC(CNC(=O)C1CCCC1)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [81, 36, 8, 8, 1, 8, 1, 1, 1, 1, 1, 81, 106, 106, 152, 152, 161, 161, 161, 161, 161, 81, 81, 81, 81, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 161] 161 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 36, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40]) total number of confs: 602 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061636 none CC(CNC(=O)C1CCCC1)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 20, 40, 67, 98, 98, 98, 160, 160, 160, 160, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 67, 67, 98, 160, 160, 160, 160, 160, 160, 160, 160, 160, 20, 20, 20, 1] 160 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: 572 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061636 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061636 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061636/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061636 Building REAL250005061637 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061637' /scratch/stefan/7916143/working/building/REAL250005061637 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061637 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061637/0 /scratch/stefan/7916143/working/building/REAL250005061637 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/767 `/scratch/stefan/7916143/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061637.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061637 none C=CCCCC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 113, 96, 18, 18, 18, 17, 17, 9, 17, 6, 9, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 186, 138, 138, 96, 96, 18, 17, 17, 17, 17, 17, 17, 9, 9, 9, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1002 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061637 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061637 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061637/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061637 Building REAL250005061638 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061638' /scratch/stefan/7916143/working/building/REAL250005061638 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061638 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061638/0 /scratch/stefan/7916143/working/building/REAL250005061638 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/768 `/scratch/stefan/7916143/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061638.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061638 none CCC(C)(C)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [160, 174, 93, 174, 174, 93, 93, 53, 37, 21, 37, 7, 21, 1, 7, 1, 1, 1, 1, 1, 1, 179, 179, 179, 179, 179, 174, 174, 174, 174, 174, 174, 93, 53, 53, 37, 37, 37, 37, 21, 21, 21, 1] 179 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: 878 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061638 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061638 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061638/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061638 Building REAL250005061639 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061639' /scratch/stefan/7916143/working/building/REAL250005061639 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061639 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061639/0 /scratch/stefan/7916143/working/building/REAL250005061639 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/769 `/scratch/stefan/7916143/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(N)=O)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061639.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061639 none CC(CNC(=O)C(N)=O)N(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', 'N.am', 'O.2', '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, 5, 8, 1, 11, 1, 8, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 72, 135, 198, 198, 198, 201, 201, 12, 38, 1, 12, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 135, 135, 198, 201, 201, 38, 38, 38, 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: 777 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061639 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061639 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061639/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061639 Building REAL250005061640 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061640' /scratch/stefan/7916143/working/building/REAL250005061640 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061640 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061640/0 /scratch/stefan/7916143/working/building/REAL250005061640 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/770 `/scratch/stefan/7916143/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1CC1C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061640.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061640 none CC(CNC(=O)CC1CC1C)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 114, 46, 46, 8, 46, 1, 1, 1, 1, 1, 164, 175, 175, 200, 200, 201, 201, 201, 201, 201, 164, 164, 164, 164, 114, 114, 46, 8, 8, 1, 1, 1, 1, 2, 2, 2, 175, 175, 175, 201] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 808 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061640 none CC(CNC(=O)CC1CC1C)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 23, 40, 68, 68, 68, 169, 201, 201, 201, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 40, 40, 68, 169, 169, 201, 201, 201, 201, 201, 201, 201, 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: 801 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061640 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061640 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061640/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061640 Building REAL250005061641 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061641' /scratch/stefan/7916143/working/building/REAL250005061641 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061641 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061641/0 /scratch/stefan/7916143/working/building/REAL250005061641 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/771 `/scratch/stefan/7916143/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NCC(C)N(C)C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005061641.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061641 none CCC1(C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 7, 7, 7, 37, 88, 88, 117, 117, 161, 161, 181, 181, 181, 181, 181, 1, 1, 4, 4, 4, 4, 4, 7, 37, 37, 88, 88, 88, 88, 117, 117, 117, 181, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 37, 38, 39, 40, 19, 20] 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, 35, 36]) total number of confs: 665 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061641 none CCC1(C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 181, 85, 85, 85, 60, 37, 23, 37, 8, 23, 1, 8, 1, 1, 1, 1, 1, 1, 181, 181, 201, 201, 201, 201, 201, 85, 60, 60, 37, 37, 37, 37, 23, 23, 23, 1, 181, 181, 181, 181] 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: 730 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061641 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061641 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061641/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061641 Building REAL250005061642 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061642' /scratch/stefan/7916143/working/building/REAL250005061642 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061642 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061642/0 /scratch/stefan/7916143/working/building/REAL250005061642 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/772 `/scratch/stefan/7916143/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)(C)C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061642.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061642 none CC(CNC(=O)C(C)(C)C)N(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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 29, 36, 46, 46, 46, 47, 47, 47, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 36, 36, 46, 47, 47, 47, 47, 47, 47, 47, 47, 47, 16, 16, 16, 1] 47 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061642 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061642 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061642/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061642 Building REAL250005061643 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061643' /scratch/stefan/7916143/working/building/REAL250005061643 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061643 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061643/0 /scratch/stefan/7916143/working/building/REAL250005061643 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/773 `/scratch/stefan/7916143/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061643.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061643 none C=C(C)CCC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 13, 13, 13, 11, 9, 8, 9, 6, 8, 1, 6, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 13, 11, 11, 9, 9, 9, 9, 8, 8, 8, 1] 24 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061643 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061643 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061643/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061643 Building REAL250005061644 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061644' /scratch/stefan/7916143/working/building/REAL250005061644 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061644 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061644/0 /scratch/stefan/7916143/working/building/REAL250005061644 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/774 `/scratch/stefan/7916143/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(CF)CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061644.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061644 none CC(CNC(=O)C1(CF)CC1)N(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.3', 'C.3', 'F', '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, 5, 5, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 7, 7, 1, 7, 1, 1, 10, 1, 1, 87, 118, 118, 179, 179, 192, 192, 192, 192, 192, 87, 87, 87, 87, 36, 36, 7, 10, 10, 1, 1, 1, 1, 118, 118, 118, 192] 201 rigid atoms, others: [32, 33, 4, 6, 7, 9, 10, 30, 31] set([0, 1, 2, 3, 5, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 719 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061644 none CC(CNC(=O)C1(CF)CC1)N(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.3', 'C.3', 'F', '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, 5, 5, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 61, 103, 103, 103, 192, 201, 192, 192, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 61, 61, 103, 201, 201, 192, 192, 192, 192, 21, 21, 21, 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: 718 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061644 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061644 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061644/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061644 Building REAL250005061645 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061645' /scratch/stefan/7916143/working/building/REAL250005061645 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061645 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061645/0 /scratch/stefan/7916143/working/building/REAL250005061645 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/775 `/scratch/stefan/7916143/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061645.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061645 none CC(C)C(C)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 163, 169, 101, 163, 101, 101, 62, 38, 22, 38, 7, 22, 1, 7, 1, 1, 1, 1, 1, 1, 169, 169, 169, 169, 169, 169, 169, 163, 163, 163, 163, 101, 62, 62, 38, 38, 38, 38, 22, 22, 22, 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: 717 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061645 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061645 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061645/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061645 Building REAL250005061646 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061646' /scratch/stefan/7916143/working/building/REAL250005061646 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061646 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061646/0 /scratch/stefan/7916143/working/building/REAL250005061646 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/776 `/scratch/stefan/7916143/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H]1C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061646.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061646 none CC[C@@H]1C[C@H]1C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 21, 21, 22, 22, 37, 37, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 1, 1, 7, 18, 18, 21, 21, 21, 21, 22, 22, 22, 39] 46 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061646 none CC[C@@H]1C[C@H]1C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 39, 39, 39, 39, 19, 39, 19, 19, 12, 10, 10, 10, 6, 10, 1, 6, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 39, 39, 19, 12, 12, 10, 10, 10, 10, 10, 10, 10, 1] 46 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: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061646 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061646 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061646/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061646 Building REAL250005061647 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061647' /scratch/stefan/7916143/working/building/REAL250005061647 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061647 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061647/0 /scratch/stefan/7916143/working/building/REAL250005061647 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/777 `/scratch/stefan/7916143/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC12CC2)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061647.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061647 none CC(CNC(=O)C1CC12CC2)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [92, 49, 12, 12, 1, 12, 1, 1, 1, 1, 1, 92, 121, 121, 165, 165, 174, 174, 174, 174, 174, 92, 92, 92, 92, 49, 49, 12, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 174] 174 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 671 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061647 none CC(CNC(=O)C1CC12CC2)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 20, 36, 62, 103, 103, 103, 174, 174, 174, 174, 9, 20, 1, 9, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 62, 62, 103, 174, 174, 174, 174, 174, 174, 174, 20, 20, 20, 1] 174 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: 628 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061647 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061647 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061647/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061647 Building REAL250005061648 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061648' /scratch/stefan/7916143/working/building/REAL250005061648 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061648 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061648/0 /scratch/stefan/7916143/working/building/REAL250005061648 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/778 `/scratch/stefan/7916143/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H]1CCCO1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061648.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061648 none CC(CNC(=O)[C@H]1CCCO1)N(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.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 5, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 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, 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: [86, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 86, 116, 116, 159, 159, 172, 172, 172, 172, 172, 86, 86, 86, 86, 37, 37, 11, 1, 1, 1, 1, 1, 1, 116, 116, 116, 172] 172 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38]) total number of confs: 622 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061648 none CC(CNC(=O)[C@H]1CCCO1)N(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.3', 'H', 'C.3', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 5, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 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, 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: [52, 26, 52, 95, 158, 158, 158, 172, 172, 172, 172, 172, 9, 26, 1, 9, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 95, 95, 158, 172, 172, 172, 172, 172, 172, 26, 26, 26, 1] 172 rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 647 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061648 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061648 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061648/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061648 Building REAL250005061649 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061649' /scratch/stefan/7916143/working/building/REAL250005061649 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061649 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061649/0 /scratch/stefan/7916143/working/building/REAL250005061649 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/779 `/scratch/stefan/7916143/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1(C)CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061649.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061649 none CC(CNC(=O)CC1(C)CC1)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 91, 32, 32, 9, 32, 1, 1, 1, 1, 1, 142, 165, 165, 199, 199, 201, 201, 201, 201, 201, 142, 142, 142, 142, 91, 91, 32, 9, 9, 2, 2, 2, 1, 1, 1, 1, 165, 165, 165, 201] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 818 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061649 none CC(CNC(=O)CC1(C)CC1)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 22, 31, 49, 90, 90, 90, 183, 201, 201, 201, 7, 22, 1, 7, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 49, 49, 90, 183, 183, 201, 201, 201, 201, 201, 201, 201, 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: 815 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061649 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061649 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061649/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061649 Building REAL250005061650 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061650' /scratch/stefan/7916143/working/building/REAL250005061650 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061650 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061650/0 /scratch/stefan/7916143/working/building/REAL250005061650 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/780 `/scratch/stefan/7916143/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(C)CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061650.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061650 none CC(CNC(=O)C1(C)CC1)N(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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 26, 7, 7, 1, 7, 1, 1, 1, 1, 50, 70, 70, 116, 116, 122, 122, 122, 122, 122, 50, 50, 50, 50, 26, 26, 7, 2, 2, 2, 1, 1, 1, 1, 70, 70, 70, 122] 122 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 443 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061650 none CC(CNC(=O)C1(C)CC1)N(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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 17, 33, 51, 68, 68, 68, 122, 122, 122, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 51, 51, 68, 122, 122, 122, 122, 122, 122, 122, 17, 17, 17, 1] 122 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: 460 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061650 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061650 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061650/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061650 Building REAL250005061651 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061651' /scratch/stefan/7916143/working/building/REAL250005061651 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061651 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061651/0 /scratch/stefan/7916143/working/building/REAL250005061651 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/781 `/scratch/stefan/7916143/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CNC=C1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061651.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061651 none CC(CNC(=O)C1=CNC=C1)N(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', 'C.2', 'N.pl3', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 1, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 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: [56, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 56, 78, 78, 112, 112, 120, 120, 120, 120, 120, 56, 56, 56, 56, 25, 25, 5, 1, 1, 1, 1, 78, 78, 78, 120] 120 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 456 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061651 none CC(CNC(=O)C1=CNC=C1)N(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', 'C.2', 'N.pl3', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 1, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 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: [37, 20, 37, 55, 79, 79, 79, 120, 120, 120, 120, 9, 20, 1, 9, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 55, 55, 79, 120, 120, 120, 120, 20, 20, 20, 1] 120 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: 387 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061651 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061651 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061651/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061651 Building REAL250005061652 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061652' /scratch/stefan/7916143/working/building/REAL250005061652 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061652 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061652/0 /scratch/stefan/7916143/working/building/REAL250005061652 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/782 `/scratch/stefan/7916143/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CN=CO1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061652.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061652 none CC(CNC(=O)C1=CN=CO1)N(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', 'C.2', 'N.2', 'C.2', 'O.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, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [30, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 30, 42, 42, 73, 73, 78, 78, 78, 78, 78, 30, 30, 30, 30, 15, 15, 6, 1, 1, 42, 42, 42, 78] 78 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061652 none CC(CNC(=O)C1=CN=CO1)N(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', 'C.2', 'N.2', 'C.2', 'O.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, 5, 8, 1, 11, 1, 1, 8, 1, 12, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [38, 17, 38, 54, 74, 74, 74, 78, 78, 78, 78, 8, 17, 1, 8, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 54, 54, 74, 78, 78, 17, 17, 17, 1] 78 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: 307 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061652 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061652 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061652/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061652 Building REAL250005061653 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061653' /scratch/stefan/7916143/working/building/REAL250005061653 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061653 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061653/0 /scratch/stefan/7916143/working/building/REAL250005061653 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/783 `/scratch/stefan/7916143/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061653.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061653 none C=CC(C)(C)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 68, 153, 153, 68, 68, 42, 26, 17, 26, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 153, 153, 153, 153, 153, 68, 42, 42, 26, 26, 26, 26, 17, 17, 17, 1] 153 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: 617 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061653 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061653 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061653/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061653 Building REAL250005061654 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061654' /scratch/stefan/7916143/working/building/REAL250005061654 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061654 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061654/0 /scratch/stefan/7916143/working/building/REAL250005061654 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/784 `/scratch/stefan/7916143/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1C[C@H]1C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061654.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061654 none CC(CNC(=O)[C@@H]1C[C@H]1C)N(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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 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, 7] dock color type numbers: [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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [80, 46, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 80, 105, 105, 149, 149, 155, 155, 155, 155, 155, 80, 80, 80, 80, 46, 46, 11, 1, 1, 2, 2, 2, 105, 105, 105, 155] 155 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061654 none CC(CNC(=O)[C@@H]1C[C@H]1C)N(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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 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, 7] dock color type numbers: [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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [38, 19, 38, 57, 86, 86, 86, 155, 155, 155, 155, 155, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 57, 57, 86, 155, 155, 155, 155, 155, 19, 19, 19, 1] 155 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: 570 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061654 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061654 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061654/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061654 Building REAL250005061655 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061655' /scratch/stefan/7916143/working/building/REAL250005061655 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061655 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061655/0 /scratch/stefan/7916143/working/building/REAL250005061655 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/785 `/scratch/stefan/7916143/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(C)CCC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061655.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061655 none CC(CNC(=O)C1(C)CCC1)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [58, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 58, 73, 73, 105, 105, 114, 114, 114, 114, 114, 58, 58, 58, 58, 28, 28, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 73, 73, 73, 114] 114 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 36, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40]) total number of confs: 438 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061655 none CC(CNC(=O)C1(C)CCC1)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 17, 29, 42, 55, 55, 55, 114, 114, 114, 114, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 42, 42, 55, 114, 114, 114, 114, 114, 114, 114, 114, 114, 17, 17, 17, 1] 114 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: 390 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061655 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061655 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061655/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061655 Building REAL250005061656 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061656' /scratch/stefan/7916143/working/building/REAL250005061656 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061656 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061656/0 /scratch/stefan/7916143/working/building/REAL250005061656 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/786 `/scratch/stefan/7916143/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061656.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061656 none CCC(F)C(=O)NCC(C)N(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', '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, 15, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 57, 36, 57, 36, 36, 20, 13, 11, 13, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 57, 36, 20, 20, 13, 13, 13, 13, 11, 11, 11, 1] 64 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: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061656 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061656 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061656/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061656 Building REAL250005061657 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061657' /scratch/stefan/7916143/working/building/REAL250005061657 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061657 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061657/0 /scratch/stefan/7916143/working/building/REAL250005061657 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/787 `/scratch/stefan/7916143/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCCF)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061657.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061657 none CC(CNC(=O)CCCF)N(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.3', 'C.3', 'C.3', 'F', '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, 5, 5, 5, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 23, 36, 70, 70, 70, 169, 198, 201, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 36, 36, 70, 169, 169, 201, 201, 201, 201, 16, 16, 16, 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: 862 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061657 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061657 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061657/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061657 Building REAL250005061658 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061658' /scratch/stefan/7916143/working/building/REAL250005061658 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061658 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061658/0 /scratch/stefan/7916143/working/building/REAL250005061658 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/788 `/scratch/stefan/7916143/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H]1C[C@@H]1C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061658.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061658 none CC(CNC(=O)[C@H]1C[C@@H]1C)N(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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 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, 7] dock color type numbers: [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 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [79, 46, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 79, 101, 101, 144, 144, 148, 148, 148, 148, 148, 79, 79, 79, 79, 46, 46, 11, 1, 1, 2, 2, 2, 101, 101, 101, 148] 148 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 564 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061658 none CC(CNC(=O)[C@H]1C[C@@H]1C)N(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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 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, 7] dock color type numbers: [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 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [36, 19, 36, 55, 86, 86, 86, 148, 148, 148, 148, 148, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 55, 55, 86, 148, 148, 148, 148, 148, 19, 19, 19, 1] 148 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: 527 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061658 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061658 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061658/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061658 Building REAL250005061659 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061659' /scratch/stefan/7916143/working/building/REAL250005061659 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061659 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061659/0 /scratch/stefan/7916143/working/building/REAL250005061659 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/789 `/scratch/stefan/7916143/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=NNN=C1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061659.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061659 none CC(CNC(=O)C1=NNN=C1)N(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', 'N.2', 'N.pl3', 'N.2', 'C.2', '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, 5, 8, 1, 11, 1, 8, 8, 8, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 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: [50, 18, 5, 5, 1, 5, 1, 1, 1, 1, 1, 50, 83, 83, 155, 155, 166, 166, 166, 166, 166, 50, 50, 50, 50, 18, 18, 5, 1, 1, 83, 83, 83, 166] 166 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 539 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061659 none CC(CNC(=O)C1=NNN=C1)N(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', 'N.2', 'N.pl3', 'N.2', 'C.2', '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, 5, 8, 1, 11, 1, 8, 8, 8, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 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: [67, 29, 67, 121, 166, 166, 166, 166, 166, 166, 166, 10, 29, 1, 10, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 121, 121, 166, 166, 166, 29, 29, 29, 1] 166 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: 666 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061659 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061659/1 /scratch/stefan/7916143/working/building/REAL250005061659 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/790 `/scratch/stefan/7916143/working/3D/790' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CN=NN1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061659.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061659 none CC(CNC(=O)C1=CN=NN1)N(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', 'C.2', 'N.2', 'N.2', 'N.pl3', '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, 5, 8, 1, 11, 1, 1, 8, 8, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 10, 10, 8, 8, 5, 1, 1, 11, 11, 11, 11] 11 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061659 none CC(CNC(=O)C1=CN=NN1)N(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', 'C.2', 'N.2', 'N.2', 'N.pl3', '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, 5, 8, 1, 11, 1, 1, 8, 8, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 8, 10, 11, 11, 11, 11, 11, 11, 11, 5, 7, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 10, 10, 11, 11, 11, 7, 7, 7, 1] 11 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: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061659 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061659 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061659/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061659/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061659 Building REAL250005061660 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061660' /scratch/stefan/7916143/working/building/REAL250005061660 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061660 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061660/0 /scratch/stefan/7916143/working/building/REAL250005061660 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/791 `/scratch/stefan/7916143/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CO)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061660.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061660 none CC(CNC(=O)CO)N(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.3', 'O.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, 8, 1, 11, 5, 12, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [17, 14, 17, 25, 38, 38, 38, 43, 7, 14, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 25, 25, 38, 43, 43, 129, 14, 14, 14, 1] 129 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: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061660 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061660 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061660/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061660 Building REAL250005061661 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061661' /scratch/stefan/7916143/working/building/REAL250005061661 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061661 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061661/0 /scratch/stefan/7916143/working/building/REAL250005061661 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/792 `/scratch/stefan/7916143/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CC(N)=O)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061661.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061661 none CC(CNC(=O)C=CC(N)=O)N(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', 'C.2', 'C.2', 'N.am', 'O.2', '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, 8, 1, 11, 1, 1, 1, 8, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [17, 12, 17, 28, 36, 36, 36, 54, 54, 58, 58, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 28, 28, 36, 54, 54, 58, 58, 12, 12, 12, 1] 58 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: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061661 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061661 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061661/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061661 Building REAL250005061662 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061662' /scratch/stefan/7916143/working/building/REAL250005061662 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061662 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061662/0 /scratch/stefan/7916143/working/building/REAL250005061662 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/793 `/scratch/stefan/7916143/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061662.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061662 none COC(=O)CC(=O)NCC(C)N(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 19, 22, 11, 11, 11, 9, 7, 7, 7, 6, 7, 1, 6, 1, 1, 1, 1, 1, 1, 22, 22, 22, 19, 19, 11, 9, 9, 7, 7, 7, 7, 7, 7, 7, 1] 22 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: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061662 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061662 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061662/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061662 Building REAL250005061663 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061663' /scratch/stefan/7916143/working/building/REAL250005061663 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061663 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061663/0 /scratch/stefan/7916143/working/building/REAL250005061663 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/794 `/scratch/stefan/7916143/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC=CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061663.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061663 none CSC=CC(=O)NCC(C)N(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', '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, 14, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 16, 15, 12, 15, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 16, 16, 15, 15, 15, 15, 12, 12, 12, 1] 24 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: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061663 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061663 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061663/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061663 Building REAL250005061664 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061664' /scratch/stefan/7916143/working/building/REAL250005061664 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061664 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061664/0 /scratch/stefan/7916143/working/building/REAL250005061664 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/795 `/scratch/stefan/7916143/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCC(N)=O)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061664.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061664 none CC(CNC(=O)CCC(N)=O)N(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.3', 'C.3', 'C.2', 'N.am', 'O.2', '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, 5, 5, 1, 8, 11, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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, 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: [19, 14, 19, 33, 60, 60, 60, 125, 152, 161, 161, 7, 14, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 33, 33, 60, 125, 125, 152, 152, 161, 161, 14, 14, 14, 1] 161 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: 704 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061664 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061664 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061664/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061664 Building REAL250005061665 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061665' /scratch/stefan/7916143/working/building/REAL250005061665 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061665 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061665/0 /scratch/stefan/7916143/working/building/REAL250005061665 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/796 `/scratch/stefan/7916143/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCO1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061665.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061665 none CC(CNC(=O)C1CCO1)N(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.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 12, 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, 7] dock color type numbers: [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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 38, 8, 8, 1, 8, 1, 1, 1, 1, 80, 116, 116, 178, 178, 201, 201, 201, 201, 201, 80, 80, 80, 80, 38, 38, 8, 1, 1, 1, 1, 1, 116, 116, 116, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 674 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061665 none CC(CNC(=O)C1CCO1)N(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.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 12, 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, 7] dock color type numbers: [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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 36, 71, 131, 191, 191, 191, 201, 201, 201, 11, 36, 1, 11, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 131, 131, 191, 201, 201, 201, 201, 201, 36, 36, 36, 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: 776 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061665 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061665 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061665/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061665 Building REAL250005061666 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061666' /scratch/stefan/7916143/working/building/REAL250005061666 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061666 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061666/0 /scratch/stefan/7916143/working/building/REAL250005061666 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/797 `/scratch/stefan/7916143/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCCO1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061666.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061666 none CC(CNC(=O)C1=CCCO1)N(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', 'C.2', 'C.3', 'C.3', 'O.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, 8, 1, 11, 1, 1, 5, 5, 12, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [56, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 56, 86, 86, 141, 141, 156, 156, 156, 156, 156, 56, 56, 56, 56, 26, 26, 6, 1, 1, 1, 1, 1, 86, 86, 86, 156] 156 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 519 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061666 none CC(CNC(=O)C1=CCCO1)N(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', 'C.2', 'C.3', 'C.3', 'O.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, 8, 1, 11, 1, 1, 5, 5, 12, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [65, 33, 65, 117, 153, 153, 153, 156, 156, 156, 156, 11, 33, 1, 11, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 117, 117, 153, 156, 156, 156, 156, 156, 33, 33, 33, 1] 156 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: 619 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061666 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061666 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061666/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061666 Building REAL250005061667 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061667' /scratch/stefan/7916143/working/building/REAL250005061667 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061667 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061667/0 /scratch/stefan/7916143/working/building/REAL250005061667 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/798 `/scratch/stefan/7916143/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1COC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061667.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061667 none CC(CNC(=O)C1COC1)N(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.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 12, 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, 7] dock color type numbers: [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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [70, 39, 9, 9, 1, 9, 1, 1, 1, 1, 70, 82, 82, 99, 99, 102, 102, 102, 102, 102, 70, 70, 70, 70, 39, 39, 9, 1, 1, 1, 1, 1, 82, 82, 82, 102] 102 rigid atoms, others: [4, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061667 none CC(CNC(=O)C1COC1)N(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.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 12, 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, 7] dock color type numbers: [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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [29, 19, 29, 49, 66, 66, 66, 102, 102, 102, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 49, 49, 66, 102, 102, 102, 102, 102, 19, 19, 19, 1] 102 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: 372 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061667 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061667 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061667/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061667 Building REAL250005061668 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061668' /scratch/stefan/7916143/working/building/REAL250005061668 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061668 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061668/0 /scratch/stefan/7916143/working/building/REAL250005061668 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/799 `/scratch/stefan/7916143/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CCO)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061668.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061668 none CC(CNC(=O)C=CCO)N(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', 'C.2', 'C.3', 'O.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, 8, 1, 11, 1, 1, 5, 12, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [34, 19, 34, 64, 106, 106, 106, 187, 187, 201, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 64, 64, 106, 187, 187, 201, 201, 603, 19, 19, 19, 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: 1381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061668 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061668 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061668/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061668 Building REAL250005061669 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061669' /scratch/stefan/7916143/working/building/REAL250005061669 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061669 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061669/0 /scratch/stefan/7916143/working/building/REAL250005061669 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/800 `/scratch/stefan/7916143/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(O)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061669.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061669 none CC=CC(O)C(=O)NCC(C)N(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', '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, 12, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 31, 27, 31, 27, 27, 15, 13, 11, 13, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 31, 93, 27, 15, 15, 13, 13, 13, 13, 11, 11, 11, 1] 120 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: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061669 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061669 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061669/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061669 Building REAL250005061670 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061670' /scratch/stefan/7916143/working/building/REAL250005061670 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061670 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061670/0 /scratch/stefan/7916143/working/building/REAL250005061670 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/801 `/scratch/stefan/7916143/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H](C)[NH+](C)C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061670.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061670 none CC(CNC(=O)[C@H](C)[NH+](C)C)N(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.3', 'H', 'C.3', 'N.4', 'H', '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, 8, 1, 11, 5, 7, 5, 9, 6, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 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, 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: [5, 5, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 1] 9 rigid atoms, others: [42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 29 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061670 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061670/1 /scratch/stefan/7916143/working/building/REAL250005061670 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/802 `/scratch/stefan/7916143/working/3D/802' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H](C)N(C)C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061670.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061670/1/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: REAL250005061670 none CC(CNC(=O)[C@H](C)N(C)C)N(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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 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, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [17, 14, 17, 24, 32, 32, 32, 42, 42, 42, 44, 44, 7, 14, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 24, 24, 32, 42, 42, 42, 44, 44, 44, 44, 44, 44, 14, 14, 14, 1] 44 rigid atoms, others: [41, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061670 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061670 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061670/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061670/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061670 Building REAL250005061671 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061671' /scratch/stefan/7916143/working/building/REAL250005061671 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061671 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061671/0 /scratch/stefan/7916143/working/building/REAL250005061671 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/803 `/scratch/stefan/7916143/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(F)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061671.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061671 none CCC=C(F)C(=O)NCC(C)N(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', '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, 1, 15, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 36, 36, 36, 36, 36, 36, 24, 18, 12, 18, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 36, 36, 24, 24, 18, 18, 18, 18, 12, 12, 12, 1] 62 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: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061671 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061671 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061671/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061671 Building REAL250005061672 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061672' /scratch/stefan/7916143/working/building/REAL250005061672 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061672 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061672/0 /scratch/stefan/7916143/working/building/REAL250005061672 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/804 `/scratch/stefan/7916143/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061672.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061672 none CCC=CC(=O)NCC(C)N(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', '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, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 27, 27, 16, 16, 16, 14, 13, 12, 13, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 27, 27, 16, 14, 14, 13, 13, 13, 13, 12, 12, 12, 1] 42 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061672 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061672 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061672/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061672 Building REAL250005061673 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061673' /scratch/stefan/7916143/working/building/REAL250005061673 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061673 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061673/0 /scratch/stefan/7916143/working/building/REAL250005061673 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/805 `/scratch/stefan/7916143/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCN=[N+]=[N-])N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061673.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061673 none CC(CNC(=O)CCN=[N+]=[N-])N(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.3', 'C.3', 'N.2', 'N.1', 'N.1', '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, 8, 1, 11, 5, 5, 8, 8, 8, 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, 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] 0 hydrogens 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, 11, 15, 27, 43, 43, 43, 137, 158, 201, 201, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 27, 27, 43, 137, 137, 158, 158, 11, 11, 11, 1] 201 rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 746 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061673 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061673 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061673/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061673 Building REAL250005061674 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061674' /scratch/stefan/7916143/working/building/REAL250005061674 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061674 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061674/0 /scratch/stefan/7916143/working/building/REAL250005061674 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/806 `/scratch/stefan/7916143/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061674.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061674 none C#CCOCC(=O)NCC(C)N(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', '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, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 149, 90, 66, 66, 66, 27, 20, 13, 20, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 90, 90, 66, 27, 27, 20, 20, 20, 20, 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: 751 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061674 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061674 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061674/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061674 Building REAL250005061675 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061675' /scratch/stefan/7916143/working/building/REAL250005061675 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061675 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061675/0 /scratch/stefan/7916143/working/building/REAL250005061675 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/807 `/scratch/stefan/7916143/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061675.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061675 none CC(O)CCC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 222 conformations in input total number of sets (complete confs): 222 using faster count positions algorithm for large data unique positions, atoms: [74, 73, 74, 74, 41, 41, 41, 28, 19, 14, 19, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 222, 74, 74, 74, 74, 41, 28, 28, 19, 19, 19, 19, 14, 14, 14, 1] 222 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: 533 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061675 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061675 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061675/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061675 Building REAL250005061676 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061676' /scratch/stefan/7916143/working/building/REAL250005061676 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061676 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061676/0 /scratch/stefan/7916143/working/building/REAL250005061676 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/808 `/scratch/stefan/7916143/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061676.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061676 none C#CCCC(=O)NCC(C)N(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', '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, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 45, 29, 29, 29, 20, 16, 12, 16, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 46, 46, 46, 45, 45, 29, 20, 20, 16, 16, 16, 16, 12, 12, 12, 1] 46 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: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061676 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061676 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061676/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061676 Building REAL250005061677 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061677' /scratch/stefan/7916143/working/building/REAL250005061677 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061677 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061677/0 /scratch/stefan/7916143/working/building/REAL250005061677 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/809 `/scratch/stefan/7916143/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC=CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061677.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061677 none CC=CC=CC(=O)NCC(C)N(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', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 19, 19, 19, 12, 11, 11, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 19, 12, 12, 11, 11, 11, 11, 11, 11, 11, 1] 24 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061677 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061677 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061677/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061677 Building REAL250005061678 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061678' /scratch/stefan/7916143/working/building/REAL250005061678 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061678 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061678/0 /scratch/stefan/7916143/working/building/REAL250005061678 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/810 `/scratch/stefan/7916143/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC=CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061678.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061678 none COCC=CC(=O)NCC(C)N(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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 68, 31, 31, 30, 30, 30, 25, 21, 15, 21, 7, 15, 1, 7, 1, 1, 1, 1, 1, 1, 73, 73, 73, 68, 68, 31, 31, 30, 25, 25, 21, 21, 21, 21, 15, 15, 15, 1] 73 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061678 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061678 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061678/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061678 Building REAL250005061679 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061679' /scratch/stefan/7916143/working/building/REAL250005061679 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061679 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061679/0 /scratch/stefan/7916143/working/building/REAL250005061679 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/811 `/scratch/stefan/7916143/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(O)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061679.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061679 none CCC(C)(O)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [46, 45, 33, 45, 45, 33, 33, 21, 15, 13, 15, 7, 13, 1, 7, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 45, 45, 45, 135, 33, 21, 21, 15, 15, 15, 15, 13, 13, 13, 1] 141 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: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061679 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061679 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061679/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061679 Building REAL250005061680 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061680' /scratch/stefan/7916143/working/building/REAL250005061680 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061680 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061680/0 /scratch/stefan/7916143/working/building/REAL250005061680 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/812 `/scratch/stefan/7916143/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061680.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061680 none C#CCC(C)C(=O)NCC(C)N(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', '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, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 39, 26, 39, 26, 26, 16, 14, 12, 14, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 43, 43, 43, 39, 39, 39, 39, 26, 16, 16, 14, 14, 14, 14, 12, 12, 12, 1] 43 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/7916143/working/building/REAL250005061680 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061680 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061680/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061680 Building REAL250005061681 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061681' /scratch/stefan/7916143/working/building/REAL250005061681 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061681 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061681/0 /scratch/stefan/7916143/working/building/REAL250005061681 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/813 `/scratch/stefan/7916143/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061681.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061681 none C=CC(O)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 37, 63, 37, 37, 21, 13, 11, 13, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 189, 37, 21, 21, 13, 13, 13, 13, 11, 11, 11, 1] 189 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: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061681 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061681 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061681/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061681 Building REAL250005061682 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061682' /scratch/stefan/7916143/working/building/REAL250005061682 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061682 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061682/0 /scratch/stefan/7916143/working/building/REAL250005061682 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/814 `/scratch/stefan/7916143/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C12CC1CC2)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061682.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061682 none CC(CNC(=O)C12CC1CC2)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [68, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 68, 98, 98, 153, 153, 167, 167, 167, 167, 167, 68, 68, 68, 68, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 167] 167 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 614 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061682 none CC(CNC(=O)C12CC1CC2)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [40, 20, 40, 63, 85, 85, 85, 167, 167, 167, 167, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 63, 63, 85, 167, 167, 167, 167, 167, 167, 167, 20, 20, 20, 1] 167 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 463 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061682 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061682 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061682/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061682 Building REAL250005061683 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061683' /scratch/stefan/7916143/working/building/REAL250005061683 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061683 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061683/0 /scratch/stefan/7916143/working/building/REAL250005061683 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/815 `/scratch/stefan/7916143/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@H](C)CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061683.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061683 none C=C[C@H](C)CC(=O)NCC(C)N(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', '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: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 66, 86, 86, 32, 32, 32, 28, 24, 17, 24, 8, 17, 1, 8, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86, 66, 66, 32, 28, 28, 24, 24, 24, 24, 17, 17, 17, 1] 86 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: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061683 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061683 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061683/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061683 Building REAL250005061684 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061684' /scratch/stefan/7916143/working/building/REAL250005061684 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061684 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061684/0 /scratch/stefan/7916143/working/building/REAL250005061684 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/816 `/scratch/stefan/7916143/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CC1CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061684.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061684 none CC(CNC(=O)C=CC1CC1)N(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', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 106, 42, 42, 10, 41, 10, 1, 1, 1, 1, 151, 167, 167, 197, 197, 201, 201, 201, 201, 201, 151, 151, 151, 151, 106, 106, 42, 10, 10, 1, 1, 1, 1, 1, 167, 167, 167, 201] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 773 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061684 none CC(CNC(=O)C=CC1CC1)N(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', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 27, 53, 87, 87, 87, 163, 163, 201, 201, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 53, 53, 87, 163, 163, 201, 201, 201, 201, 201, 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: 721 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061684 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061684 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061684/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061684 Building REAL250005061685 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061685' /scratch/stefan/7916143/working/building/REAL250005061685 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061685 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061685/0 /scratch/stefan/7916143/working/building/REAL250005061685 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/817 `/scratch/stefan/7916143/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C#N)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061685.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061685 none CCC(C#N)C(=O)NCC(C)N(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [91, 94, 51, 94, 94, 51, 51, 31, 20, 16, 20, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 94, 51, 31, 31, 20, 20, 20, 20, 16, 16, 16, 1] 100 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: 497 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061685 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061685 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061685/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061685 Building REAL250005061686 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061686' /scratch/stefan/7916143/working/building/REAL250005061686 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061686 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061686/0 /scratch/stefan/7916143/working/building/REAL250005061686 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/818 `/scratch/stefan/7916143/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1C2CCC21)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061686.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061686 none CC(CNC(=O)C1C2CCC21)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [49, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 49, 58, 58, 91, 91, 94, 94, 94, 94, 94, 49, 49, 49, 49, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 94] 94 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061686 none CC(CNC(=O)C1C2CCC21)N(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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 19, 33, 54, 80, 80, 80, 94, 94, 94, 94, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 54, 54, 80, 94, 94, 94, 94, 94, 94, 94, 19, 19, 19, 1] 94 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: 361 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061686 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061686 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061686/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061686 Building REAL250005061687 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061687' /scratch/stefan/7916143/working/building/REAL250005061687 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061687 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061687/0 /scratch/stefan/7916143/working/building/REAL250005061687 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/819 `/scratch/stefan/7916143/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC1C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061687.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061687 none C=C1CCC1C(=O)NCC(C)N(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', '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, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 36, 72, 72, 98, 98, 139, 139, 149, 149, 149, 149, 149, 1, 1, 1, 1, 1, 1, 1, 9, 36, 36, 72, 72, 72, 72, 98, 98, 98, 149] 149 rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 22, 23, 24, 25, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 555 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061687 none C=C1CCC1C(=O)NCC(C)N(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', '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, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 122, 122, 122, 72, 42, 20, 42, 9, 20, 1, 9, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 149, 149, 149, 122, 72, 72, 42, 42, 42, 42, 20, 20, 20, 1] 149 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: 577 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061687 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061687 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061687/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061687 Building REAL250005061688 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061688' /scratch/stefan/7916143/working/building/REAL250005061688 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061688 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061688/0 /scratch/stefan/7916143/working/building/REAL250005061688 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/820 `/scratch/stefan/7916143/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1[C@H](C)[C@@H]1C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061688.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061688 none CC(CNC(=O)C1[C@H](C)[C@@H]1C)N(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.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 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, 7, 7, 7] dock color type numbers: [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, 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: [63, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 63, 89, 89, 136, 136, 145, 145, 145, 145, 145, 63, 63, 63, 63, 26, 26, 7, 1, 2, 2, 2, 2, 2, 2, 89, 89, 89, 145] 145 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 5, 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: 531 number of broken/clashed sets: 145 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061688 none CC(CNC(=O)C1[C@H](C)[C@@H]1C)N(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.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 7, 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, 7, 7, 7] dock color type numbers: [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, 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: [46, 22, 46, 85, 123, 123, 123, 145, 145, 145, 145, 145, 145, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 85, 85, 123, 145, 145, 145, 145, 145, 145, 145, 22, 22, 22, 1] 145 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: 567 number of broken/clashed sets: 145 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061688 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061688 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061688/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061688 Building REAL250005061689 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061689' /scratch/stefan/7916143/working/building/REAL250005061689 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005061689 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061689/0 /scratch/stefan/7916143/working/building/REAL250005061689 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/821 `/scratch/stefan/7916143/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061689.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061689 none CC[N@H+](C)CC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 4, 4, 4, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 1] 7 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: 29 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061689 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061689/1 /scratch/stefan/7916143/working/building/REAL250005061689 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/822 `/scratch/stefan/7916143/working/3D/822' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061689.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061689/1/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: REAL250005061689 none CC[N@@H+](C)CC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 1] 6 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: 23 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061689 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `2' /scratch/stefan/7916143/working/building/REAL250005061689/2 /scratch/stefan/7916143/working/building/REAL250005061689 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 2 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/823 `/scratch/stefan/7916143/working/3D/823' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061689.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005061689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061689/2/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: REAL250005061689 none CCN(C)CC(=O)NCC(C)N(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', '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, 10, 5, 5, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 68, 68, 58, 58, 58, 35, 23, 16, 23, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 68, 68, 68, 68, 68, 58, 35, 35, 23, 23, 23, 23, 16, 16, 16, 1] 69 rigid atoms, others: [41, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061689 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061689 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061689/0.* 2: /scratch/stefan/7916143/working/building/REAL250005061689/2.* 1: /scratch/stefan/7916143/working/building/REAL250005061689/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061689 Building REAL250005061690 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061690' /scratch/stefan/7916143/working/building/REAL250005061690 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061690 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061690/0 /scratch/stefan/7916143/working/building/REAL250005061690 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/824 `/scratch/stefan/7916143/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061690.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061690 none CC(O)C(=O)NCC(C)N(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', '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, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [45, 32, 45, 32, 32, 23, 15, 13, 15, 7, 13, 1, 7, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 135, 32, 23, 23, 15, 15, 15, 15, 13, 13, 13, 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: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061690 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061690 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061690/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061690 Building REAL250005061691 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061691' /scratch/stefan/7916143/working/building/REAL250005061691 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061691 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061691/0 /scratch/stefan/7916143/working/building/REAL250005061691 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/825 `/scratch/stefan/7916143/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061691.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061691 none CC(=O)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 11, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 201, 195, 195, 127, 65, 32, 65, 10, 32, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 127, 127, 65, 65, 65, 65, 32, 32, 32, 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: 771 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061691 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061691 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061691/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061691 Building REAL250005061692 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061692' /scratch/stefan/7916143/working/building/REAL250005061692 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061692 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061692/0 /scratch/stefan/7916143/working/building/REAL250005061692 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/826 `/scratch/stefan/7916143/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCCC#N)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061692.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061692 none CC(CNC(=O)CCCC#N)N(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.3', 'C.3', 'C.3', 'C.1', 'N.1', '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, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 17, 29, 56, 56, 56, 159, 172, 201, 201, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 29, 29, 56, 159, 159, 187, 187, 195, 198, 13, 13, 13, 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: 934 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061692 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061692 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061692/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061692 Building REAL250005061693 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061693' /scratch/stefan/7916143/working/building/REAL250005061693 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061693 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061693/0 /scratch/stefan/7916143/working/building/REAL250005061693 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/827 `/scratch/stefan/7916143/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(C#N)CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061693.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061693 none CC(CNC(=O)C1(C#N)CC1)N(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.3', 'C.1', 'N.1', '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, 8, 1, 11, 5, 1, 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, 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] 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: [45, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 45, 58, 58, 82, 82, 85, 85, 85, 85, 85, 45, 45, 45, 45, 21, 21, 6, 1, 1, 1, 1, 58, 58, 58, 85] 85 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 318 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061693 none CC(CNC(=O)C1(C#N)CC1)N(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.3', 'C.1', 'N.1', '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, 8, 1, 11, 5, 1, 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, 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] 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: [29, 16, 29, 44, 71, 71, 71, 85, 85, 85, 85, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 44, 44, 71, 85, 85, 85, 85, 16, 16, 16, 1] 85 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: 327 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061693 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061693 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061693/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061693 Building REAL250005061694 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061694' /scratch/stefan/7916143/working/building/REAL250005061694 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061694 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061694/0 /scratch/stefan/7916143/working/building/REAL250005061694 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/828 `/scratch/stefan/7916143/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C(=O)NCC(C)N(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061694.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061694 none C=C1CC(C(=O)NCC(C)N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 22, 24, 24, 26, 26, 38, 38, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 7, 22, 22, 24, 24, 24, 24, 26, 26, 26, 40, 1, 1] 40 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 20, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061694 none C=C1CC(C(=O)NCC(C)N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 18, 18, 18, 14, 11, 11, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 18, 14, 14, 11, 11, 11, 11, 11, 11, 11, 1, 40, 40] 40 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: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061694 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061694 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061694/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061694 Building REAL250005061695 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061695' /scratch/stefan/7916143/working/building/REAL250005061695 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061695 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061695/0 /scratch/stefan/7916143/working/building/REAL250005061695 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/829 `/scratch/stefan/7916143/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(F)CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061695.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061695 none CC(CNC(=O)C1(F)CC1)N(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.3', 'F', '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, 8, 1, 11, 5, 15, 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, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [59, 42, 13, 13, 1, 13, 1, 1, 1, 1, 59, 62, 62, 69, 69, 69, 69, 69, 69, 69, 59, 59, 59, 59, 42, 42, 13, 1, 1, 1, 1, 62, 62, 62, 69] 69 rigid atoms, others: [4, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 278 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061695 none CC(CNC(=O)C1(F)CC1)N(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.3', 'F', '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, 8, 1, 11, 5, 15, 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, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 17, 28, 44, 44, 44, 69, 69, 69, 7, 13, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 28, 28, 44, 69, 69, 69, 69, 13, 13, 13, 1] 69 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 250 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061695 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061695 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061695/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061695 Building REAL250005061696 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061696' /scratch/stefan/7916143/working/building/REAL250005061696 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061696 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061696/0 /scratch/stefan/7916143/working/building/REAL250005061696 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/830 `/scratch/stefan/7916143/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061696.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061696 none COC(C)(C)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 91, 47, 91, 91, 47, 47, 25, 14, 12, 14, 7, 12, 1, 7, 1, 1, 1, 1, 1, 1, 93, 93, 93, 91, 91, 91, 91, 91, 91, 47, 25, 25, 14, 14, 14, 14, 12, 12, 12, 1] 93 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: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061696 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061696 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061696/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061696 Building REAL250005061697 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061697' /scratch/stefan/7916143/working/building/REAL250005061697 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061697 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061697/0 /scratch/stefan/7916143/working/building/REAL250005061697 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/831 `/scratch/stefan/7916143/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC#N)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061697.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061697 none CC(CC#N)C(=O)NCC(C)N(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [127, 57, 127, 158, 158, 57, 57, 33, 19, 14, 19, 7, 14, 1, 7, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 158, 158, 57, 33, 33, 19, 19, 19, 19, 14, 14, 14, 1] 158 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: 711 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061697 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061697 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061697/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061697 Building REAL250005061698 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061698' /scratch/stefan/7916143/working/building/REAL250005061698 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061698 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061698/0 /scratch/stefan/7916143/working/building/REAL250005061698 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/832 `/scratch/stefan/7916143/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CC1C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061698.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061698 none CCC1CC1C(=O)NCC(C)N(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', '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, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 6, 6, 6, 22, 28, 28, 34, 34, 39, 39, 41, 41, 41, 41, 41, 2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 22, 22, 28, 28, 28, 28, 34, 34, 34, 41] 41 rigid atoms, others: [1, 2, 3, 4, 5, 26, 27, 28, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061698 none CCC1CC1C(=O)NCC(C)N(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', '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, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 32, 32, 32, 20, 15, 11, 15, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 32, 20, 20, 15, 15, 15, 15, 11, 11, 11, 1] 41 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: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061698 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061698 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061698/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061698 Building REAL250005061699 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061699' /scratch/stefan/7916143/working/building/REAL250005061699 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061699 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061699/0 /scratch/stefan/7916143/working/building/REAL250005061699 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/833 `/scratch/stefan/7916143/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061699.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061699 none C=CC(C)(O)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 25, 35, 35, 25, 25, 16, 12, 10, 12, 6, 10, 1, 6, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 105, 25, 16, 16, 12, 12, 12, 12, 10, 10, 10, 1] 105 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: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061699 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061699 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061699/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061699 Building REAL250005061700 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061700' /scratch/stefan/7916143/working/building/REAL250005061700 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061700 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061700/0 /scratch/stefan/7916143/working/building/REAL250005061700 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/834 `/scratch/stefan/7916143/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC=CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061700.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061700 none CCCC=CC(=O)NCC(C)N(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', '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, 1, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 17, 17, 10, 10, 10, 10, 7, 6, 7, 5, 6, 1, 5, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 29, 29, 17, 17, 10, 10, 10, 7, 7, 7, 7, 6, 6, 6, 1] 30 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: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061700 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061700 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061700/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061700 Building REAL250005061701 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061701' /scratch/stefan/7916143/working/building/REAL250005061701 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061701 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061701/0 /scratch/stefan/7916143/working/building/REAL250005061701 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/835 `/scratch/stefan/7916143/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061701.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061701 none CC=C(F)C(=O)NCC(C)N(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', '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, 1, 15, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 118, 127, 118, 118, 84, 49, 21, 49, 9, 21, 1, 9, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 118, 84, 84, 49, 49, 49, 49, 21, 21, 21, 1] 127 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 507 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061701 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061701 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061701/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061701 Building REAL250005061702 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061702' /scratch/stefan/7916143/working/building/REAL250005061702 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061702 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061702/0 /scratch/stefan/7916143/working/building/REAL250005061702 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/836 `/scratch/stefan/7916143/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H](C)[NH+](C)C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061702.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061702 none CC(CNC(=O)[C@@H](C)[NH+](C)C)N(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.3', 'H', 'C.3', 'N.4', 'H', '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, 8, 1, 11, 5, 7, 5, 9, 6, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 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, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 7, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 1] 8 rigid atoms, others: [42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 23 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061702 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061702/1 /scratch/stefan/7916143/working/building/REAL250005061702 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/837 `/scratch/stefan/7916143/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H](C)N(C)C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061702.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061702/1/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: REAL250005061702 none CC(CNC(=O)[C@@H](C)N(C)C)N(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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 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, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [17, 14, 17, 24, 37, 37, 37, 44, 44, 44, 47, 47, 7, 14, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 24, 24, 37, 44, 44, 44, 47, 47, 47, 47, 47, 47, 14, 14, 14, 1] 47 rigid atoms, others: [41, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061702 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061702 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061702/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061702/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061702 Building REAL250005061703 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061703' /scratch/stefan/7916143/working/building/REAL250005061703 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061703 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061703/0 /scratch/stefan/7916143/working/building/REAL250005061703 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/838 `/scratch/stefan/7916143/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC=CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061703.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061703 none CCOC=CC(=O)NCC(C)N(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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 18, 18, 18, 18, 18, 18, 14, 13, 11, 13, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 18, 18, 18, 14, 14, 13, 13, 13, 13, 11, 11, 11, 1] 19 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061703 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061703 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061703/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061703 Building REAL250005061704 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061704' /scratch/stefan/7916143/working/building/REAL250005061704 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061704 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061704/0 /scratch/stefan/7916143/working/building/REAL250005061704 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/839 `/scratch/stefan/7916143/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)OCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061704.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061704 none CC(=O)OCC(=O)NCC(C)N(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 5, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 52, 32, 32, 32, 24, 15, 12, 15, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 56, 56, 56, 52, 52, 32, 24, 24, 15, 15, 15, 15, 12, 12, 12, 1] 56 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: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061704 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061704 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061704/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061704 Building REAL250005061705 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061705' /scratch/stefan/7916143/working/building/REAL250005061705 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061705 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061705/0 /scratch/stefan/7916143/working/building/REAL250005061705 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/840 `/scratch/stefan/7916143/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C=CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061705.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061705 none CC(=O)C=CC(=O)NCC(C)N(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 21, 16, 13, 16, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 21, 21, 16, 16, 16, 16, 13, 13, 13, 1] 32 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061705 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061705 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061705/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061705 Building REAL250005061706 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061706' /scratch/stefan/7916143/working/building/REAL250005061706 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061706 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061706/0 /scratch/stefan/7916143/working/building/REAL250005061706 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/841 `/scratch/stefan/7916143/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)COC1CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061706.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061706 none CC(CNC(=O)COC1CC1)N(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.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 167, 97, 97, 26, 97, 6, 1, 1, 1, 1, 188, 189, 189, 201, 201, 201, 201, 201, 201, 201, 188, 188, 188, 188, 167, 167, 97, 26, 26, 1, 1, 1, 1, 1, 189, 189, 189, 201] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 773 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061706 none CC(CNC(=O)COC1CC1)N(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.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 13, 24, 52, 52, 52, 156, 185, 201, 201, 7, 11, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 24, 24, 52, 156, 156, 201, 201, 201, 201, 201, 11, 11, 11, 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: 707 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061706 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061706 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061706/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061706 Building REAL250005061707 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061707' /scratch/stefan/7916143/working/building/REAL250005061707 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061707 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061707/0 /scratch/stefan/7916143/working/building/REAL250005061707 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/842 `/scratch/stefan/7916143/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=NC=CN1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061707.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061707 none CC(CNC(=O)C1=NC=CN1)N(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', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 1, 8, 1, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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: [55, 15, 3, 3, 1, 3, 1, 1, 1, 1, 1, 57, 102, 102, 182, 182, 201, 201, 201, 201, 201, 57, 57, 57, 57, 15, 15, 3, 1, 1, 1, 102, 102, 102, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 646 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061707 none CC(CNC(=O)C1=NC=CN1)N(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', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 1, 8, 1, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [42, 27, 42, 54, 64, 64, 64, 66, 66, 66, 66, 12, 27, 1, 12, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 54, 54, 64, 66, 66, 66, 27, 27, 27, 1] 66 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: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061707 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061707 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061707/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061707 Building REAL250005061708 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061708' /scratch/stefan/7916143/working/building/REAL250005061708 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061708 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061708/0 /scratch/stefan/7916143/working/building/REAL250005061708 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/843 `/scratch/stefan/7916143/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061708.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061708 none CC(CO)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [199, 121, 199, 199, 121, 121, 69, 41, 22, 41, 7, 22, 1, 7, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 199, 199, 597, 121, 69, 69, 41, 41, 41, 41, 22, 22, 22, 1] 597 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: 1439 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061708 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061708 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061708/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061708 Building REAL250005061709 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061709' /scratch/stefan/7916143/working/building/REAL250005061709 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061709 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061709/0 /scratch/stefan/7916143/working/building/REAL250005061709 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/844 `/scratch/stefan/7916143/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CON=C1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061709.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061709 none CC(CNC(=O)C1=CON=C1)N(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', 'C.2', 'O.3', 'N.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 12, 8, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [52, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 52, 77, 77, 105, 105, 108, 108, 108, 108, 108, 52, 52, 52, 52, 25, 25, 5, 1, 1, 77, 77, 77, 108] 108 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 420 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061709 none CC(CNC(=O)C1=CON=C1)N(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', 'C.2', 'O.3', 'N.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 12, 8, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [36, 20, 36, 48, 69, 69, 69, 108, 108, 108, 108, 9, 20, 1, 9, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 48, 48, 69, 108, 108, 20, 20, 20, 1] 108 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: 346 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061709 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061709 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061709/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061709 Building REAL250005061710 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061710' /scratch/stefan/7916143/working/building/REAL250005061710 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061710 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061710/0 /scratch/stefan/7916143/working/building/REAL250005061710 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/845 `/scratch/stefan/7916143/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCCCO)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061710.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061710 none CC(CNC(=O)CCCCO)N(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.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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, 7, 7] 1 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [13, 11, 13, 16, 27, 27, 27, 51, 54, 55, 55, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 16, 16, 27, 51, 51, 55, 55, 55, 55, 55, 55, 165, 11, 11, 11, 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: 386 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061710 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061710 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061710/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061710 Building REAL250005061711 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061711' /scratch/stefan/7916143/working/building/REAL250005061711 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061711 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061711/0 /scratch/stefan/7916143/working/building/REAL250005061711 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/846 `/scratch/stefan/7916143/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(=O)C1CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061711.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061711 none CC(CNC(=O)C(=O)C1CC1)N(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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 5, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [75, 68, 41, 41, 12, 41, 1, 12, 1, 1, 1, 75, 75, 75, 76, 76, 76, 76, 76, 76, 76, 75, 75, 75, 75, 68, 68, 41, 1, 1, 1, 1, 1, 75, 75, 75, 76] 76 rigid atoms, others: [32, 6, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061711 none CC(CNC(=O)C(=O)C1CC1)N(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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 5, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [11, 10, 11, 17, 35, 35, 35, 59, 59, 76, 76, 6, 10, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 17, 17, 35, 76, 76, 76, 76, 76, 10, 10, 10, 1] 76 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: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061711 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061711 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061711/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061711 Building REAL250005061712 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061712' /scratch/stefan/7916143/working/building/REAL250005061712 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061712 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061712/0 /scratch/stefan/7916143/working/building/REAL250005061712 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/847 `/scratch/stefan/7916143/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC1(O)CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061712.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061712 none CC(CNC(=O)CC1(O)CC1)N(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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 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, 6, 7, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [165, 119, 44, 44, 10, 44, 1, 1, 1, 1, 1, 165, 181, 181, 199, 199, 201, 201, 201, 201, 201, 165, 165, 165, 165, 119, 119, 44, 10, 10, 6, 1, 1, 1, 1, 181, 181, 181, 201] 603 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 816 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061712 none CC(CNC(=O)CC1(O)CC1)N(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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 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, 6, 7, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [26, 18, 26, 45, 78, 78, 78, 175, 201, 201, 201, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 45, 45, 78, 175, 175, 603, 201, 201, 201, 201, 18, 18, 18, 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: 1419 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061712 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061712 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061712/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061712 Building REAL250005061713 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061713' /scratch/stefan/7916143/working/building/REAL250005061713 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061713 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061713/0 /scratch/stefan/7916143/working/building/REAL250005061713 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/848 `/scratch/stefan/7916143/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CCC1F)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061713.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061713 none CC(CNC(=O)C1CCC1F)N(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.3', 'C.3', 'C.3', 'C.3', 'F', '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, 5, 5, 5, 5, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [51, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 51, 62, 62, 82, 82, 89, 89, 89, 89, 89, 51, 51, 51, 51, 33, 33, 9, 1, 1, 1, 1, 1, 1, 62, 62, 62, 89] 89 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061713 none CC(CNC(=O)C1CCC1F)N(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.3', 'C.3', 'C.3', 'C.3', 'F', '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, 5, 5, 5, 5, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 16, 29, 43, 67, 67, 67, 89, 89, 89, 89, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 43, 43, 67, 89, 89, 89, 89, 89, 89, 16, 16, 16, 1] 89 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: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061713 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061713 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061713/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061713 Building REAL250005061714 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061714' /scratch/stefan/7916143/working/building/REAL250005061714 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061714 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061714/0 /scratch/stefan/7916143/working/building/REAL250005061714 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/849 `/scratch/stefan/7916143/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1C[C@H]1CF)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061714.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061714 none CC(CNC(=O)[C@@H]1C[C@H]1CF)N(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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', '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, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 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, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [112, 56, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 9, 112, 140, 140, 182, 182, 190, 190, 190, 190, 190, 112, 112, 112, 112, 56, 56, 12, 1, 1, 9, 9, 140, 140, 140, 190] 192 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 766 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061714 none CC(CNC(=O)[C@@H]1C[C@H]1CF)N(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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', '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, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 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, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [27, 18, 27, 47, 81, 81, 81, 190, 190, 190, 190, 190, 192, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 47, 47, 81, 190, 190, 192, 192, 18, 18, 18, 1] 192 rigid atoms, others: [37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 616 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061714 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061714 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061714/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061714 Building REAL250005061715 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061715' /scratch/stefan/7916143/working/building/REAL250005061715 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061715 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061715/0 /scratch/stefan/7916143/working/building/REAL250005061715 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/850 `/scratch/stefan/7916143/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CO)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061715.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061715 none CCC(CO)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [112, 114, 66, 114, 117, 66, 66, 40, 24, 16, 24, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 114, 117, 117, 351, 66, 40, 40, 24, 24, 24, 24, 16, 16, 16, 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: 908 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061715 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061715 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061715/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061715 Building REAL250005061716 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061716' /scratch/stefan/7916143/working/building/REAL250005061716 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061716 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061716/0 /scratch/stefan/7916143/working/building/REAL250005061716 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/851 `/scratch/stefan/7916143/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1C[C@@H]1C#N)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061716.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061716 none CC(CNC(=O)[C@@H]1C[C@@H]1C#N)N(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.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [42, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 42, 53, 53, 83, 83, 89, 89, 89, 89, 89, 42, 42, 42, 42, 25, 25, 7, 1, 1, 53, 53, 53, 89] 89 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061716 none CC(CNC(=O)[C@@H]1C[C@@H]1C#N)N(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.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [30, 18, 30, 47, 73, 73, 73, 89, 89, 89, 89, 89, 89, 9, 18, 1, 9, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 47, 47, 73, 89, 89, 18, 18, 18, 1] 89 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: 361 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061716 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061716 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061716/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061716 Building REAL250005061717 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061717' /scratch/stefan/7916143/working/building/REAL250005061717 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061717 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061717/0 /scratch/stefan/7916143/working/building/REAL250005061717 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/852 `/scratch/stefan/7916143/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=COCC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061717.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061717 none CC(CNC(=O)C1=COCC1)N(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', 'C.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 26, 28, 28, 37, 37, 38, 38, 38, 38, 38, 26, 26, 26, 26, 19, 19, 5, 1, 1, 1, 1, 1, 28, 28, 28, 38] 38 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061717 none CC(CNC(=O)C1=COCC1)N(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', 'C.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 12, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 16, 22, 29, 29, 29, 38, 38, 38, 38, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 22, 29, 38, 38, 38, 38, 38, 12, 12, 12, 1] 38 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: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061717 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061717 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061717/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061717 Building REAL250005061718 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061718' /scratch/stefan/7916143/working/building/REAL250005061718 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061718 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061718/0 /scratch/stefan/7916143/working/building/REAL250005061718 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/853 `/scratch/stefan/7916143/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(O)CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061718.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061718 none CC(CNC(=O)C1(O)CC1)N(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.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 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, 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] 1 hydrogens need rotated 288 conformations in input total number of sets (complete confs): 288 using faster count positions algorithm for large data unique positions, atoms: [76, 50, 12, 12, 1, 12, 1, 1, 1, 1, 76, 84, 84, 94, 94, 96, 96, 96, 96, 96, 76, 76, 76, 76, 50, 50, 12, 6, 1, 1, 1, 1, 84, 84, 84, 96] 288 rigid atoms, others: [4, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061718 none CC(CNC(=O)C1(O)CC1)N(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.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 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, 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] 1 hydrogens need rotated 288 conformations in input total number of sets (complete confs): 288 using faster count positions algorithm for large data unique positions, atoms: [25, 17, 25, 37, 59, 59, 59, 96, 96, 96, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 37, 37, 59, 288, 96, 96, 96, 96, 17, 17, 17, 1] 288 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: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061718 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061718 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061718/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061718 Building REAL250005061719 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061719' /scratch/stefan/7916143/working/building/REAL250005061719 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061719 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061719/0 /scratch/stefan/7916143/working/building/REAL250005061719 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/854 `/scratch/stefan/7916143/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CCC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061719.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061719 none CC(CNC(=O)C1=CCC1)N(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', 'C.2', '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, 8, 1, 11, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 11, 4, 4, 1, 4, 1, 1, 1, 1, 26, 40, 40, 57, 57, 59, 59, 59, 59, 59, 26, 26, 26, 26, 11, 11, 4, 1, 1, 1, 1, 1, 40, 40, 40, 59] 59 rigid atoms, others: [4, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061719 none CC(CNC(=O)C1=CCC1)N(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', 'C.2', '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, 8, 1, 11, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 18, 32, 46, 59, 59, 59, 59, 59, 59, 9, 18, 1, 9, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 46, 46, 59, 59, 59, 59, 59, 59, 18, 18, 18, 1] 59 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061719 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061719 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061719/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061719 Building REAL250005061720 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061720' /scratch/stefan/7916143/working/building/REAL250005061720 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061720 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061720/0 /scratch/stefan/7916143/working/building/REAL250005061720 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/855 `/scratch/stefan/7916143/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061720.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061720 none CC(CF)C(=O)NCC(C)N(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', '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, 15, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [187, 109, 187, 187, 109, 109, 63, 40, 23, 40, 7, 23, 1, 7, 1, 1, 1, 1, 1, 1, 187, 187, 187, 187, 187, 187, 109, 63, 63, 40, 40, 40, 40, 23, 23, 23, 1] 187 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: 767 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061720 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061720 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061720/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061720 Building REAL250005061721 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061721' /scratch/stefan/7916143/working/building/REAL250005061721 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061721 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061721/0 /scratch/stefan/7916143/working/building/REAL250005061721 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/856 `/scratch/stefan/7916143/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061721.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061721 none CC=CC(=O)NCC(C)N(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', '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, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 60, 60, 60, 46, 31, 18, 31, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 60, 46, 46, 31, 31, 31, 31, 18, 18, 18, 1] 75 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: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061721 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061721 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061721/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061721 Building REAL250005061722 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061722' /scratch/stefan/7916143/working/building/REAL250005061722 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061722 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061722/0 /scratch/stefan/7916143/working/building/REAL250005061722 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/857 `/scratch/stefan/7916143/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(C)CC1F)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061722.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061722 none CC(CNC(=O)C1(C)CC1F)N(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.3', 'C.3', 'C.3', 'C.3', 'F', '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, 5, 5, 5, 5, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 52, 75, 75, 121, 121, 136, 136, 136, 136, 136, 52, 52, 52, 52, 24, 24, 6, 2, 2, 2, 1, 1, 1, 75, 75, 75, 136] 136 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 472 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061722 none CC(CNC(=O)C1(C)CC1F)N(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.3', 'C.3', 'C.3', 'C.3', 'F', '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, 5, 5, 5, 5, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 18, 40, 65, 101, 101, 101, 136, 136, 136, 136, 8, 18, 1, 8, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 65, 65, 101, 136, 136, 136, 136, 136, 136, 18, 18, 18, 1] 136 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 /scratch/stefan/7916143/working/building/REAL250005061722 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061722 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061722/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061722 Building REAL250005061723 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061723' /scratch/stefan/7916143/working/building/REAL250005061723 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061723 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061723/0 /scratch/stefan/7916143/working/building/REAL250005061723 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/858 `/scratch/stefan/7916143/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C=CCF)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061723.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061723 none CC(CNC(=O)C=CCF)N(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', 'C.2', 'C.3', 'F', '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, 8, 1, 11, 1, 1, 5, 15, 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, 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 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [25, 15, 25, 45, 69, 69, 69, 108, 108, 122, 7, 15, 1, 7, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 45, 69, 108, 108, 122, 122, 15, 15, 15, 1] 122 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: 490 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061723 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061723 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061723/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061723 Building REAL250005061724 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061724' /scratch/stefan/7916143/working/building/REAL250005061724 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061724 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061724/0 /scratch/stefan/7916143/working/building/REAL250005061724 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/859 `/scratch/stefan/7916143/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(CO)CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061724.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061724 none CC(CNC(=O)C1(CO)CC1)N(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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 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, 6, 7, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [89, 35, 7, 7, 1, 7, 1, 1, 8, 1, 1, 89, 121, 121, 180, 180, 189, 189, 189, 189, 189, 89, 89, 89, 89, 35, 35, 7, 8, 8, 24, 1, 1, 1, 1, 121, 121, 121, 189] 603 rigid atoms, others: [32, 33, 34, 4, 6, 7, 9, 10, 31] set([0, 1, 2, 3, 5, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 740 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061724 none CC(CNC(=O)C1(CO)CC1)N(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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 12, 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, 6, 7, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [34, 19, 34, 59, 106, 106, 106, 189, 201, 189, 189, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 59, 59, 106, 201, 201, 603, 189, 189, 189, 189, 19, 19, 19, 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: 1320 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061724 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061724 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061724/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061724 Building REAL250005061725 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061725' /scratch/stefan/7916143/working/building/REAL250005061725 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061725 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061725/0 /scratch/stefan/7916143/working/building/REAL250005061725 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/860 `/scratch/stefan/7916143/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC=NO1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061725.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061725 none CC(CNC(=O)C1=CC=NO1)N(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', 'C.2', 'C.2', 'N.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 8, 12, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [67, 29, 6, 6, 1, 6, 1, 1, 1, 1, 1, 67, 104, 104, 167, 167, 180, 180, 180, 180, 180, 67, 67, 67, 67, 28, 28, 6, 1, 1, 104, 104, 104, 180] 180 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 617 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061725 none CC(CNC(=O)C1=CC=NO1)N(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', 'C.2', 'C.2', 'N.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 8, 12, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [67, 30, 67, 124, 170, 170, 170, 179, 179, 179, 179, 12, 30, 1, 12, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 124, 124, 170, 179, 179, 30, 30, 30, 1] 179 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: 696 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061725 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061725 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061725/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061725 Building REAL250005061726 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061726' /scratch/stefan/7916143/working/building/REAL250005061726 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005061726 as failed and skipping /scratch/stefan/7916143/working /scratch/stefan/7916143 `/scratch/stefan/7916143/working/building/REAL250005061726' -> `/scratch/stefan/7916143/failed/REAL250005061726' Building REAL250005061727 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061727' /scratch/stefan/7916143/working/building/REAL250005061727 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061727 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061727/0 /scratch/stefan/7916143/working/building/REAL250005061727 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/861 `/scratch/stefan/7916143/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H](C)O)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061727.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061727 none CC(CNC(=O)[C@H](C)O)N(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.3', 'H', 'C.3', 'O.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, 8, 1, 11, 5, 7, 5, 12, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [15, 13, 15, 23, 34, 34, 34, 46, 46, 46, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 23, 23, 34, 46, 46, 46, 138, 13, 13, 13, 1] 138 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: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061727 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061727 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061727/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061727 Building REAL250005061728 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061728' /scratch/stefan/7916143/working/building/REAL250005061728 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061728 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061728/0 /scratch/stefan/7916143/working/building/REAL250005061728 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/862 `/scratch/stefan/7916143/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061728.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061728 none CON=CC(=O)NCC(C)N(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', '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, 8, 1, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 61, 61, 61, 40, 23, 15, 23, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 61, 40, 40, 23, 23, 23, 23, 15, 15, 15, 1] 63 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061728 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061728 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061728/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061728 Building REAL250005061729 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061729' /scratch/stefan/7916143/working/building/REAL250005061729 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061729 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061729/0 /scratch/stefan/7916143/working/building/REAL250005061729 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/863 `/scratch/stefan/7916143/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](O)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061729.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061729 none CC(C)[C@H](O)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 228 conformations in input total number of sets (complete confs): 228 using faster count positions algorithm for large data unique positions, atoms: [76, 73, 76, 44, 73, 73, 44, 44, 24, 14, 12, 14, 7, 12, 1, 7, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 76, 76, 219, 44, 24, 24, 14, 14, 14, 14, 12, 12, 12, 1] 228 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: 531 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061729 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061729 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061729/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061729 Building REAL250005061730 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061730' /scratch/stefan/7916143/working/building/REAL250005061730 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061730 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061730/0 /scratch/stefan/7916143/working/building/REAL250005061730 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/864 `/scratch/stefan/7916143/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)NCC(C)N(C)C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005061730.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061730 none C#CC1(C(=O)NCC(C)N(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', '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: [1, 1, 5, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 32, 81, 81, 113, 113, 187, 187, 201, 201, 201, 201, 201, 1, 1, 1, 7, 32, 32, 81, 81, 81, 81, 113, 113, 113, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 36, 35, 33, 34, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 719 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061730 none C#CC1(C(=O)NCC(C)N(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', '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: [1, 1, 5, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 100, 100, 100, 75, 43, 20, 43, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 100, 75, 75, 43, 43, 43, 43, 20, 20, 20, 1, 201, 201, 201, 201] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 707 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061730 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061730 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061730/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061730 Building REAL250005061731 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061731' /scratch/stefan/7916143/working/building/REAL250005061731 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061731 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061731/0 /scratch/stefan/7916143/working/building/REAL250005061731 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/865 `/scratch/stefan/7916143/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC=CCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061731.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061731 none C=CC=CCC(=O)NCC(C)N(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', '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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 30, 15, 15, 15, 11, 11, 9, 11, 6, 9, 1, 6, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 30, 30, 15, 11, 11, 11, 11, 11, 11, 9, 9, 9, 1] 35 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061731 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061731 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061731/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061731 Building REAL250005061732 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061732' /scratch/stefan/7916143/working/building/REAL250005061732 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061732 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061732/0 /scratch/stefan/7916143/working/building/REAL250005061732 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/866 `/scratch/stefan/7916143/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#C[C@H]1C[C@H]1C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061732.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061732 none C#C[C@H]1C[C@H]1C(=O)NCC(C)N(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', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 26, 26, 34, 34, 40, 40, 42, 42, 42, 42, 42, 1, 1, 1, 6, 23, 23, 26, 26, 26, 26, 34, 34, 34, 42] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061732 none C#C[C@H]1C[C@H]1C(=O)NCC(C)N(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', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 31, 42, 31, 31, 20, 15, 11, 15, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 42, 42, 42, 31, 20, 20, 15, 15, 15, 15, 11, 11, 11, 1] 42 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: 158 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061732 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061732 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061732/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061732 Building REAL250005061733 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061733' /scratch/stefan/7916143/working/building/REAL250005061733 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061733 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061733/0 /scratch/stefan/7916143/working/building/REAL250005061733 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/867 `/scratch/stefan/7916143/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(CC)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061733.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061733 none CC=C(CC)C(=O)NCC(C)N(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', '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, 1, 5, 5, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 73, 156, 201, 73, 73, 50, 28, 18, 28, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 201, 201, 201, 201, 201, 73, 50, 50, 28, 28, 28, 28, 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: 806 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061733 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061733 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061733/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061733 Building REAL250005061734 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061734' /scratch/stefan/7916143/working/building/REAL250005061734 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061734 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061734/0 /scratch/stefan/7916143/working/building/REAL250005061734 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/868 `/scratch/stefan/7916143/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(F)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061734.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061734 none COC(F)C(=O)NCC(C)N(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', '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, 15, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 19, 31, 19, 19, 11, 8, 8, 8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 1, 32, 32, 32, 31, 19, 11, 11, 8, 8, 8, 8, 8, 8, 8, 1] 32 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: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061734 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061734 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061734/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061734 Building REAL250005061735 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061735' /scratch/stefan/7916143/working/building/REAL250005061735 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061735 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061735/0 /scratch/stefan/7916143/working/building/REAL250005061735 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/869 `/scratch/stefan/7916143/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1C[C@H]1C#N)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061735.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061735 none CC(CNC(=O)[C@@H]1C[C@H]1C#N)N(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.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [53, 38, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 53, 66, 66, 84, 84, 85, 85, 85, 85, 85, 53, 53, 53, 53, 38, 38, 11, 1, 1, 66, 66, 66, 85] 85 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061735 none CC(CNC(=O)[C@@H]1C[C@H]1C#N)N(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.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [24, 16, 24, 34, 51, 51, 51, 85, 85, 85, 85, 85, 85, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 34, 34, 51, 85, 85, 16, 16, 16, 1] 85 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: 306 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061735 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061735 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061735/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061735 Building REAL250005061736 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061736' /scratch/stefan/7916143/working/building/REAL250005061736 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061736 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061736/0 /scratch/stefan/7916143/working/building/REAL250005061736 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/870 `/scratch/stefan/7916143/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H]1C[C@@H](O)C1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061736.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061736 none CC(CNC(=O)[C@H]1C[C@@H](O)C1)N(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.3', 'H', 'C.3', 'C.3', 'H', 'O.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, 8, 1, 11, 5, 7, 5, 5, 7, 12, 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] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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] 1 hydrogens need rotated 291 conformations in input total number of sets (complete confs): 291 using faster count positions algorithm for large data unique positions, atoms: [57, 38, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 57, 69, 69, 92, 92, 97, 97, 97, 97, 97, 57, 57, 57, 57, 38, 38, 10, 1, 1, 3, 1, 1, 69, 69, 69, 97] 291 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37, 38]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061736 none CC(CNC(=O)[C@H]1C[C@@H](O)C1)N(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.3', 'H', 'C.3', 'C.3', 'H', 'O.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, 8, 1, 11, 5, 7, 5, 5, 7, 12, 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] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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] 1 hydrogens need rotated 291 conformations in input total number of sets (complete confs): 291 using faster count positions algorithm for large data unique positions, atoms: [27, 16, 27, 38, 61, 61, 61, 97, 97, 97, 97, 97, 97, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 38, 38, 61, 97, 97, 291, 97, 97, 16, 16, 16, 1] 291 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: 635 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061736 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061736 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061736/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061736 Building REAL250005061737 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061737' /scratch/stefan/7916143/working/building/REAL250005061737 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061737 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061737/0 /scratch/stefan/7916143/working/building/REAL250005061737 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/871 `/scratch/stefan/7916143/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)(C)CO)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061737.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061737 none CC(CNC(=O)C(C)(C)CO)N(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.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 5, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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, 7, 7] 1 hydrogens need rotated 516 conformations in input total number of sets (complete confs): 516 using faster count positions algorithm for large data unique positions, atoms: [40, 23, 40, 66, 111, 111, 111, 170, 170, 170, 172, 8, 23, 1, 8, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 66, 66, 111, 170, 170, 170, 170, 170, 170, 172, 172, 516, 23, 23, 23, 1] 516 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: 1237 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061737 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061737 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061737/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061737 Building REAL250005061738 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061738' /scratch/stefan/7916143/working/building/REAL250005061738 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061738 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061738/0 /scratch/stefan/7916143/working/building/REAL250005061738 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/872 `/scratch/stefan/7916143/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061738.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061738 none C=CCC(C)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 73, 40, 73, 40, 40, 30, 23, 16, 23, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 102, 73, 73, 73, 73, 40, 30, 30, 23, 23, 23, 23, 16, 16, 16, 1] 102 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: 482 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061738 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061738 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061738/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061738 Building REAL250005061739 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061739' /scratch/stefan/7916143/working/building/REAL250005061739 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061739 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061739/0 /scratch/stefan/7916143/working/building/REAL250005061739 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/873 `/scratch/stefan/7916143/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1C[C@H]1C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061739.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061739 none CC(CNC(=O)[C@@H]1C[C@H]1C)N(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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 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, 7] dock color type numbers: [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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [80, 46, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 80, 105, 105, 149, 149, 155, 155, 155, 155, 155, 80, 80, 80, 80, 46, 46, 11, 1, 1, 2, 2, 2, 105, 105, 105, 155] 155 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061739 none CC(CNC(=O)[C@@H]1C[C@H]1C)N(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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 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, 7] dock color type numbers: [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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [38, 19, 38, 57, 86, 86, 86, 155, 155, 155, 155, 155, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 57, 57, 86, 155, 155, 155, 155, 155, 19, 19, 19, 1] 155 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: 570 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061739 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061739 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061739/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061739 Building REAL250005061740 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061740' /scratch/stefan/7916143/working/building/REAL250005061740 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061740 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061740/0 /scratch/stefan/7916143/working/building/REAL250005061740 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/874 `/scratch/stefan/7916143/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)(C)O)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061740.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061740 none CC(CNC(=O)C(C)(C)O)N(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.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 12, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [13, 11, 13, 18, 28, 28, 28, 41, 41, 41, 7, 11, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 18, 18, 28, 41, 41, 41, 41, 41, 41, 123, 11, 11, 11, 1] 123 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: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061740 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061740 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061740/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061740 Building REAL250005061741 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061741' /scratch/stefan/7916143/working/building/REAL250005061741 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061741 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061741/0 /scratch/stefan/7916143/working/building/REAL250005061741 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/875 `/scratch/stefan/7916143/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=NOCC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061741.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061741 none CC(CNC(=O)C1=NOCC1)N(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', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 12, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 13, 13, 1, 13, 1, 1, 1, 1, 1, 94, 135, 135, 191, 191, 201, 201, 201, 201, 201, 94, 94, 94, 94, 44, 44, 13, 1, 1, 1, 1, 135, 135, 135, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 724 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061741 none CC(CNC(=O)C1=NOCC1)N(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', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 12, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 62, 127, 191, 191, 191, 201, 201, 201, 201, 12, 32, 1, 12, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 127, 127, 191, 201, 201, 201, 201, 32, 32, 32, 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: 747 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061741 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061741 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061741/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061741 Building REAL250005061742 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061742' /scratch/stefan/7916143/working/building/REAL250005061742 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061742 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061742/0 /scratch/stefan/7916143/working/building/REAL250005061742 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/876 `/scratch/stefan/7916143/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061742.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061742 none CC(C#N)CC(=O)NCC(C)N(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 5, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [153, 145, 154, 154, 56, 56, 56, 31, 18, 14, 18, 7, 14, 1, 7, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 145, 145, 56, 31, 31, 18, 18, 18, 18, 14, 14, 14, 1] 154 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 653 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061742 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061742 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061742/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061742 Building REAL250005061743 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061743' /scratch/stefan/7916143/working/building/REAL250005061743 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061743 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061743/0 /scratch/stefan/7916143/working/building/REAL250005061743 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/877 `/scratch/stefan/7916143/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCO)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061743.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061743 none CC(CCO)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [55, 33, 55, 57, 57, 33, 33, 22, 18, 14, 18, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 57, 57, 57, 57, 171, 33, 22, 22, 18, 18, 18, 18, 14, 14, 14, 1] 171 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: 417 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061743 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061743 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061743/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061743 Building REAL250005061744 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061744' /scratch/stefan/7916143/working/building/REAL250005061744 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061744 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061744/0 /scratch/stefan/7916143/working/building/REAL250005061744 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/878 `/scratch/stefan/7916143/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H](O)CF)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061744.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061744 none CC(CNC(=O)[C@H](O)CF)N(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.3', 'H', 'O.3', 'C.3', 'F', '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, 8, 1, 11, 5, 7, 12, 5, 15, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [14, 12, 14, 21, 31, 31, 31, 51, 51, 51, 51, 7, 12, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 21, 21, 31, 153, 51, 51, 12, 12, 12, 1] 153 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: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061744 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061744 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061744/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061744 Building REAL250005061745 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061745' /scratch/stefan/7916143/working/building/REAL250005061745 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061745 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061745/0 /scratch/stefan/7916143/working/building/REAL250005061745 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/879 `/scratch/stefan/7916143/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(O)CCC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061745.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061745 none CC(CNC(=O)C1(O)CCC1)N(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.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [84, 38, 7, 7, 1, 7, 1, 1, 1, 1, 1, 84, 125, 125, 184, 184, 201, 201, 201, 201, 201, 84, 84, 84, 84, 38, 38, 7, 6, 1, 1, 1, 1, 1, 1, 125, 125, 125, 201] 603 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38]) total number of confs: 727 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061745 none CC(CNC(=O)C1(O)CCC1)N(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.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 24, 53, 105, 177, 177, 177, 201, 201, 201, 201, 10, 24, 1, 10, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 105, 105, 177, 603, 201, 201, 201, 201, 201, 201, 24, 24, 24, 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: 1365 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061745 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061745 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061745/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061745 Building REAL250005061746 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061746' /scratch/stefan/7916143/working/building/REAL250005061746 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061746 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061746/0 /scratch/stefan/7916143/working/building/REAL250005061746 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/880 `/scratch/stefan/7916143/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(O)C1CC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061746.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061746 none CC(CNC(=O)C(O)C1CC1)N(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.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 237 conformations in input total number of sets (complete confs): 237 using faster count positions algorithm for large data unique positions, atoms: [74, 62, 29, 29, 8, 29, 1, 8, 1, 1, 1, 74, 76, 76, 79, 79, 79, 79, 79, 79, 79, 74, 74, 74, 74, 62, 62, 29, 8, 24, 1, 1, 1, 1, 1, 76, 76, 76, 79] 237 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061746 none CC(CNC(=O)C(O)C1CC1)N(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.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 237 conformations in input total number of sets (complete confs): 237 using faster count positions algorithm for large data unique positions, atoms: [14, 12, 14, 24, 44, 44, 44, 69, 69, 79, 79, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 24, 24, 44, 69, 207, 79, 79, 79, 79, 79, 12, 12, 12, 1] 237 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 528 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061746 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061746 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061746/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061746 Building REAL250005061747 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061747' /scratch/stefan/7916143/working/building/REAL250005061747 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061747 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061747/0 /scratch/stefan/7916143/working/building/REAL250005061747 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/881 `/scratch/stefan/7916143/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061747.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061747 none C=C(C)CC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 146, 148, 72, 72, 72, 42, 27, 19, 27, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 148, 146, 146, 72, 42, 42, 27, 27, 27, 27, 19, 19, 19, 1] 148 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: 625 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061747 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061747 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061747/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061747 Building REAL250005061748 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061748' /scratch/stefan/7916143/working/building/REAL250005061748 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061748 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061748/0 /scratch/stefan/7916143/working/building/REAL250005061748 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/882 `/scratch/stefan/7916143/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(C)(C)C#N)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061748.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061748 none CC(CNC(=O)C(C)(C)C#N)N(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.3', 'C.3', 'C.3', 'C.1', 'N.1', '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, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 28, 50, 84, 146, 146, 146, 180, 180, 180, 180, 12, 28, 1, 12, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 84, 84, 146, 180, 180, 180, 180, 180, 180, 28, 28, 28, 1] 180 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: 722 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061748 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061748 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061748/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061748 Building REAL250005061749 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061749' /scratch/stefan/7916143/working/building/REAL250005061749 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061749 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061749/0 /scratch/stefan/7916143/working/building/REAL250005061749 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/883 `/scratch/stefan/7916143/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061749.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061749 none CC(C)=C(C)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 119, 144, 119, 119, 71, 40, 21, 40, 9, 21, 1, 9, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 144, 144, 144, 144, 144, 119, 71, 71, 40, 40, 40, 40, 21, 21, 21, 1] 144 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: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061749 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061749 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061749/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061749 Building REAL250005061750 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061750' /scratch/stefan/7916143/working/building/REAL250005061750 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061750 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061750/0 /scratch/stefan/7916143/working/building/REAL250005061750 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/884 `/scratch/stefan/7916143/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061750.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061750 none CNC(=O)CC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 40, 40, 40, 26, 16, 13, 16, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 40, 26, 26, 16, 16, 16, 16, 13, 13, 13, 1] 48 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061750 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061750 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061750/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061750 Building REAL250005061751 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061751' /scratch/stefan/7916143/working/building/REAL250005061751 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061751 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061751/0 /scratch/stefan/7916143/working/building/REAL250005061751 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/885 `/scratch/stefan/7916143/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC(F)C1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061751.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061751 none CC(CNC(=O)C1CC(F)C1)N(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.3', 'C.3', 'C.3', 'F', '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, 5, 5, 5, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 39, 11, 11, 1, 11, 1, 1, 1, 1, 1, 61, 76, 76, 104, 104, 110, 110, 110, 110, 110, 61, 61, 61, 61, 39, 39, 11, 1, 1, 1, 1, 1, 1, 76, 76, 76, 110] 110 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37]) total number of confs: 411 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061751 none CC(CNC(=O)C1CC(F)C1)N(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.3', 'C.3', 'C.3', 'F', '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, 5, 5, 5, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 18, 29, 44, 68, 68, 68, 110, 110, 110, 110, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 44, 44, 68, 110, 110, 110, 110, 110, 110, 18, 18, 18, 1] 110 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: 397 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061751 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061751 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061751/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061751 Building REAL250005061752 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061752' /scratch/stefan/7916143/working/building/REAL250005061752 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061752 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061752/0 /scratch/stefan/7916143/working/building/REAL250005061752 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/886 `/scratch/stefan/7916143/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061752.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061752 none C=CCC(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 71, 71, 71, 39, 24, 16, 24, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 120, 71, 39, 39, 24, 24, 24, 24, 16, 16, 16, 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: 523 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061752 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061752 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061752/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061752 Building REAL250005061753 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061753' /scratch/stefan/7916143/working/building/REAL250005061753 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061753 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061753/0 /scratch/stefan/7916143/working/building/REAL250005061753 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/887 `/scratch/stefan/7916143/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C[NH+](C)C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061753.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061753 none CC(CNC(=O)C[NH+](C)C)N(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.3', 'N.4', 'H', '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, 8, 1, 11, 5, 9, 6, 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, 7, 7, 7, 7] dock color type numbers: [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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 9, 11, 11, 11, 11, 11, 11, 11, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 1] 11 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: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061753 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061753/1 /scratch/stefan/7916143/working/building/REAL250005061753 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/888 `/scratch/stefan/7916143/working/3D/888' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN(C)C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061753.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061753/1/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: REAL250005061753 none CC(CNC(=O)CN(C)C)N(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.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 10, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 13, 15, 27, 51, 51, 51, 96, 104, 104, 7, 13, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 27, 27, 51, 96, 96, 104, 104, 104, 104, 104, 104, 13, 13, 13, 1] 104 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: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061753 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061753 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061753/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061753/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061753 Building REAL250005061754 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061754' /scratch/stefan/7916143/working/building/REAL250005061754 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061754 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061754/0 /scratch/stefan/7916143/working/building/REAL250005061754 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/889 `/scratch/stefan/7916143/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CC#N)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061754.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061754 none CC(CNC(=O)CC#N)N(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.3', 'C.1', 'N.1', '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, 5, 8, 1, 11, 5, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [20, 16, 20, 29, 45, 45, 45, 64, 64, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 29, 29, 45, 64, 64, 16, 16, 16, 1] 64 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: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061754 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061754 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061754/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061754 Building REAL250005061755 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061755' /scratch/stefan/7916143/working/building/REAL250005061755 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061755 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061755/0 /scratch/stefan/7916143/working/building/REAL250005061755 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/890 `/scratch/stefan/7916143/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC1F)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061755.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061755 none CC(CNC(=O)C1CC1F)N(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.3', 'C.3', 'C.3', 'F', '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, 8, 1, 11, 5, 5, 5, 15, 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, 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 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [104, 57, 12, 12, 1, 12, 1, 1, 1, 1, 104, 130, 130, 162, 162, 167, 167, 167, 167, 167, 104, 104, 104, 104, 57, 57, 12, 1, 1, 1, 1, 130, 130, 130, 167] 167 rigid atoms, others: [4, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 645 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061755 none CC(CNC(=O)C1CC1F)N(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.3', 'C.3', 'C.3', 'F', '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, 8, 1, 11, 5, 5, 5, 15, 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, 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 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [40, 21, 40, 65, 102, 102, 102, 167, 167, 167, 7, 21, 1, 7, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 65, 65, 102, 167, 167, 167, 167, 21, 21, 21, 1] 167 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: 598 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061755 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061755 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061755/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061755 Building REAL250005061756 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061756' /scratch/stefan/7916143/working/building/REAL250005061756 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061756 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061756/0 /scratch/stefan/7916143/working/building/REAL250005061756 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/891 `/scratch/stefan/7916143/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H](C)[NH+](C)C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061756.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061756 none CC(CNC(=O)[C@H](C)[NH+](C)C)N(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.3', 'H', 'C.3', 'N.4', 'H', '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, 8, 1, 11, 5, 7, 5, 9, 6, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 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, 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: [5, 5, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 1] 9 rigid atoms, others: [42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 29 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061756 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061756/1 /scratch/stefan/7916143/working/building/REAL250005061756 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/892 `/scratch/stefan/7916143/working/3D/892' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H](C)N(C)C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061756.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061756/1/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: REAL250005061756 none CC(CNC(=O)[C@H](C)N(C)C)N(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.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 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, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [17, 14, 17, 24, 32, 32, 32, 42, 42, 42, 44, 44, 7, 14, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 24, 24, 32, 42, 42, 42, 44, 44, 44, 44, 44, 44, 14, 14, 14, 1] 44 rigid atoms, others: [41, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061756 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061756 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061756/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061756/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061756 Building REAL250005061757 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061757' /scratch/stefan/7916143/working/building/REAL250005061757 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061757 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061757/0 /scratch/stefan/7916143/working/building/REAL250005061757 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/893 `/scratch/stefan/7916143/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CCF)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061757.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061757 none CC(CNC(=O)CCF)N(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.3', 'C.3', 'F', '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, 8, 1, 11, 5, 5, 15, 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, 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 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [39, 22, 39, 65, 103, 103, 103, 159, 159, 7, 22, 1, 7, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 65, 65, 103, 159, 159, 159, 159, 22, 22, 22, 1] 159 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: 673 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061757 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061757 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061757/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061757 Building REAL250005061758 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061758' /scratch/stefan/7916143/working/building/REAL250005061758 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061758 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061758/0 /scratch/stefan/7916143/working/building/REAL250005061758 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/894 `/scratch/stefan/7916143/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1C=CCC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061758.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061758 none CC(CNC(=O)C1C=CCC1)N(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.3', 'C.2', 'C.2', '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, 8, 1, 11, 5, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [85, 44, 10, 10, 1, 10, 1, 1, 1, 1, 1, 85, 112, 112, 165, 165, 172, 172, 172, 172, 172, 85, 85, 85, 85, 44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 172] 172 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 638 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061758 none CC(CNC(=O)C1C=CCC1)N(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.3', 'C.2', 'C.2', '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, 8, 1, 11, 5, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [37, 20, 37, 59, 93, 93, 93, 172, 172, 172, 172, 7, 20, 1, 7, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 59, 59, 93, 172, 172, 172, 172, 172, 172, 172, 20, 20, 20, 1] 172 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: 602 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061758 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061758 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061758/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061758 Building REAL250005061759 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061759' /scratch/stefan/7916143/working/building/REAL250005061759 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061759 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061759/0 /scratch/stefan/7916143/working/building/REAL250005061759 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/895 `/scratch/stefan/7916143/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC(C)(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061759.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061759 none C#CC(C)(C)C(=O)NCC(C)N(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', '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, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 106, 173, 173, 106, 106, 73, 45, 20, 45, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 173, 173, 173, 173, 173, 173, 173, 106, 73, 73, 45, 45, 45, 45, 20, 20, 20, 1] 173 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: 778 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061759 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061759 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061759/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061759 Building REAL250005061760 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061760' /scratch/stefan/7916143/working/building/REAL250005061760 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061760 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061760/0 /scratch/stefan/7916143/working/building/REAL250005061760 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/896 `/scratch/stefan/7916143/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061760.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061760 none CO[C@H](C)C(=O)NCC(C)N(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', '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, 12, 5, 7, 5, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 36, 58, 58, 36, 36, 25, 15, 13, 15, 7, 13, 1, 7, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58, 36, 25, 25, 15, 15, 15, 15, 13, 13, 13, 1] 58 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: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061760 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061760 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061760/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061760 Building REAL250005061761 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061761' /scratch/stefan/7916143/working/building/REAL250005061761 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061761 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061761/0 /scratch/stefan/7916143/working/building/REAL250005061761 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/897 `/scratch/stefan/7916143/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)CCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061761.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061761 none CC(=O)CCC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 57, 38, 38, 38, 28, 17, 14, 17, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 57, 57, 38, 28, 28, 17, 17, 17, 17, 14, 14, 14, 1] 58 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061761 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061761 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061761/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061761 Building REAL250005061762 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061762' /scratch/stefan/7916143/working/building/REAL250005061762 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061762 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061762/0 /scratch/stefan/7916143/working/building/REAL250005061762 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/898 `/scratch/stefan/7916143/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H](C)O)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061762.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061762 none CC(CNC(=O)[C@@H](C)O)N(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.3', 'H', 'C.3', 'O.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, 8, 1, 11, 5, 7, 5, 12, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [15, 13, 15, 23, 32, 32, 32, 45, 45, 45, 7, 13, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 23, 23, 32, 45, 45, 45, 135, 13, 13, 13, 1] 135 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061762 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061762 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061762/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061762 Building REAL250005061763 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061763' /scratch/stefan/7916143/working/building/REAL250005061763 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005061763 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061763/0 /scratch/stefan/7916143/working/building/REAL250005061763 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/899 `/scratch/stefan/7916143/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)CN1CCC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061763.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061763 none CC(CNC(=O)CN1CCC1)N(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.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 10, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [91, 71, 28, 28, 7, 28, 1, 1, 1, 1, 1, 91, 95, 95, 98, 98, 98, 98, 98, 98, 98, 91, 91, 91, 91, 71, 71, 28, 7, 7, 1, 1, 1, 1, 1, 1, 95, 95, 95, 98] 98 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061763 none CC(CNC(=O)CN1CCC1)N(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.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 10, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 13, 16, 27, 50, 50, 50, 82, 98, 98, 98, 7, 13, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 27, 27, 50, 82, 82, 98, 98, 98, 98, 98, 98, 13, 13, 13, 1] 98 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: 376 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061763 /scratch/stefan/7916143/working /scratch/stefan/7916143 mkdir: created directory `1' /scratch/stefan/7916143/working/building/REAL250005061763/1 /scratch/stefan/7916143/working/building/REAL250005061763 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 1 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/900 `/scratch/stefan/7916143/working/3D/900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C[NH+]1CCC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061763.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005061763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061763 none CC(CNC(=O)C[NH+]1CCC1)N(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.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 16, 16, 16, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 17 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061763 none CC(CNC(=O)C[NH+]1CCC1)N(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.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 11, 17, 17, 17, 17, 17, 17, 17, 17, 7, 9, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 1] 17 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 53 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061763 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061763 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061763/0.* 1: /scratch/stefan/7916143/working/building/REAL250005061763/1.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061763 Building REAL250005061764 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061764' /scratch/stefan/7916143/working/building/REAL250005061764 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061764 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061764/0 /scratch/stefan/7916143/working/building/REAL250005061764 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/901 `/scratch/stefan/7916143/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(C)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061764.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061764 none CC(O)C(C)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 495 conformations in input total number of sets (complete confs): 495 using faster count positions algorithm for large data unique positions, atoms: [165, 140, 165, 89, 140, 89, 89, 52, 31, 19, 31, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 495, 140, 140, 140, 140, 89, 52, 52, 31, 31, 31, 31, 19, 19, 19, 1] 495 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: 1230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061764 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061764 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061764/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061764 Building REAL250005061765 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061765' /scratch/stefan/7916143/working/building/REAL250005061765 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061765 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061765/0 /scratch/stefan/7916143/working/building/REAL250005061765 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/902 `/scratch/stefan/7916143/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061765.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061765 none C=C1CC1C(=O)NCC(C)N(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', '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, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 57, 103, 103, 137, 137, 187, 187, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 13, 57, 57, 103, 103, 103, 103, 137, 137, 137, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 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]) total number of confs: 759 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061765 none C=C1CC1C(=O)NCC(C)N(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', '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, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 125, 125, 83, 50, 24, 50, 10, 24, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 125, 83, 83, 50, 50, 50, 50, 24, 24, 24, 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: 723 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061765 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061765 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061765/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061765 Building REAL250005061766 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061766' /scratch/stefan/7916143/working/building/REAL250005061766 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061766 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061766/0 /scratch/stefan/7916143/working/building/REAL250005061766 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/903 `/scratch/stefan/7916143/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(C)COC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061766.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061766 none CC(CNC(=O)C1(C)COC1)N(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.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 12, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [30, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 30, 35, 35, 47, 47, 49, 49, 49, 49, 49, 30, 30, 30, 30, 22, 22, 4, 2, 2, 2, 1, 1, 1, 1, 35, 35, 35, 49] 49 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061766 none CC(CNC(=O)C1(C)COC1)N(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.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 12, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 16, 18, 25, 25, 25, 49, 49, 49, 49, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 18, 18, 25, 49, 49, 49, 49, 49, 49, 49, 12, 12, 12, 1] 49 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: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061766 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061766 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061766/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061766 Building REAL250005061767 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061767' /scratch/stefan/7916143/working/building/REAL250005061767 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061767 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061767/0 /scratch/stefan/7916143/working/building/REAL250005061767 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/904 `/scratch/stefan/7916143/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC(=O)N1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061767.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061767 none CC(CNC(=O)C1CC(=O)N1)N(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.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 8, 1, 11, 5, 5, 1, 11, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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] 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: [46, 27, 10, 10, 1, 10, 1, 1, 1, 1, 1, 46, 56, 56, 74, 74, 78, 78, 78, 78, 78, 46, 46, 46, 46, 27, 27, 10, 1, 1, 1, 1, 56, 56, 56, 78] 78 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061767 none CC(CNC(=O)C1CC(=O)N1)N(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.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 8, 1, 11, 5, 5, 1, 11, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 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] 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: [27, 16, 27, 43, 63, 63, 63, 78, 78, 78, 78, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 43, 43, 63, 78, 78, 78, 78, 16, 16, 16, 1] 78 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: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061767 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061767 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061767/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061767 Building REAL250005061768 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061768' /scratch/stefan/7916143/working/building/REAL250005061768 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061768 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061768/0 /scratch/stefan/7916143/working/building/REAL250005061768 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/905 `/scratch/stefan/7916143/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@@H]1CC(=O)N1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061768.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061768 none CC(CNC(=O)[C@@H]1CC(=O)N1)N(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.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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, 8, 1, 11, 5, 7, 5, 1, 11, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 21, 21, 28, 28, 28, 28, 28, 28, 28, 19, 19, 19, 19, 16, 16, 6, 1, 1, 1, 21, 21, 21, 28] 28 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061768 none CC(CNC(=O)[C@@H]1CC(=O)N1)N(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.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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, 8, 1, 11, 5, 7, 5, 1, 11, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 15, 22, 24, 24, 24, 28, 28, 28, 28, 28, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 22, 22, 24, 28, 28, 28, 11, 11, 11, 1] 28 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: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061768 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061768 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061768/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061768 Building REAL250005061769 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061769' /scratch/stefan/7916143/working/building/REAL250005061769 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061769 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061769/0 /scratch/stefan/7916143/working/building/REAL250005061769 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/906 `/scratch/stefan/7916143/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](O)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061769.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061769 none CCC[C@H](O)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 45, 37, 45, 45, 37, 37, 20, 15, 11, 15, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 135, 37, 20, 20, 15, 15, 15, 15, 11, 11, 11, 1] 165 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: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061769 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061769 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061769/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061769 Building REAL250005061770 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061770' /scratch/stefan/7916143/working/building/REAL250005061770 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061770 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061770/0 /scratch/stefan/7916143/working/building/REAL250005061770 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/907 `/scratch/stefan/7916143/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(F)CCC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061770.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061770 none CC(CNC(=O)C1(F)CCC1)N(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.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 15, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 10, 10, 1, 10, 1, 1, 1, 1, 1, 90, 125, 125, 187, 187, 201, 201, 201, 201, 201, 90, 90, 90, 90, 45, 45, 10, 1, 1, 1, 1, 1, 1, 125, 125, 125, 201] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37]) total number of confs: 715 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061770 none CC(CNC(=O)C1(F)CCC1)N(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.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 15, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 49, 96, 164, 164, 164, 201, 201, 201, 201, 9, 21, 1, 9, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 96, 96, 164, 201, 201, 201, 201, 201, 201, 21, 21, 21, 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: 763 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061770 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061770 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061770/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061770 Building REAL250005061771 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061771' /scratch/stefan/7916143/working/building/REAL250005061771 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061771 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061771/0 /scratch/stefan/7916143/working/building/REAL250005061771 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/908 `/scratch/stefan/7916143/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CN=CN1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061771.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061771 none CC(CNC(=O)C1=CN=CN1)N(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', 'C.2', 'N.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 1, 1, 8, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [48, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 48, 66, 66, 95, 95, 105, 105, 105, 105, 105, 48, 48, 48, 48, 23, 23, 6, 1, 1, 1, 66, 66, 66, 105] 105 rigid atoms, others: [4, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061771 none CC(CNC(=O)C1=CN=CN1)N(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', 'C.2', 'N.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 1, 1, 8, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [50, 26, 50, 74, 100, 100, 100, 105, 105, 105, 105, 11, 26, 1, 11, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 74, 74, 100, 105, 105, 105, 26, 26, 26, 1] 105 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: 404 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061771 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061771 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061771/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061771 Building REAL250005061772 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061772' /scratch/stefan/7916143/working/building/REAL250005061772 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061772 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061772/0 /scratch/stefan/7916143/working/building/REAL250005061772 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/909 `/scratch/stefan/7916143/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CC(=O)C1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061772.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061772 none CC(CNC(=O)C1CC(=O)C1)N(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.3', 'C.3', 'C.2', 'O.2', '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, 8, 1, 11, 5, 5, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [47, 30, 10, 10, 1, 10, 1, 1, 1, 1, 1, 47, 56, 56, 72, 72, 74, 74, 74, 74, 74, 47, 47, 47, 47, 30, 30, 10, 1, 1, 1, 1, 1, 56, 56, 56, 74] 74 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061772 none CC(CNC(=O)C1CC(=O)C1)N(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.3', 'C.3', 'C.2', 'O.2', '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, 8, 1, 11, 5, 5, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [23, 16, 23, 33, 47, 47, 47, 74, 74, 74, 74, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 33, 33, 47, 74, 74, 74, 74, 74, 16, 16, 16, 1] 74 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 /scratch/stefan/7916143/working/building/REAL250005061772 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061772 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061772/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061772 Building REAL250005061773 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061773' /scratch/stefan/7916143/working/building/REAL250005061773 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061773 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061773/0 /scratch/stefan/7916143/working/building/REAL250005061773 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/910 `/scratch/stefan/7916143/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1(O)COC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061773.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061773 none CC(CNC(=O)C1(O)COC1)N(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.3', 'O.3', 'C.3', 'O.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, 8, 1, 11, 5, 12, 5, 12, 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, 7, 4, 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] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [34, 24, 8, 8, 1, 8, 1, 1, 1, 1, 1, 34, 37, 37, 41, 41, 41, 41, 41, 41, 41, 34, 34, 34, 34, 24, 24, 8, 6, 1, 1, 1, 1, 37, 37, 37, 41] 123 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 174 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061773 none CC(CNC(=O)C1(O)COC1)N(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.3', 'O.3', 'C.3', 'O.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, 8, 1, 11, 5, 12, 5, 12, 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, 7, 4, 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] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [15, 13, 15, 21, 28, 28, 28, 41, 41, 41, 41, 7, 13, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 21, 21, 28, 123, 41, 41, 41, 41, 13, 13, 13, 1] 123 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: 272 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061773 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061773 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061773/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061773 Building REAL250005061774 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061774' /scratch/stefan/7916143/working/building/REAL250005061774 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061774 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061774/0 /scratch/stefan/7916143/working/building/REAL250005061774 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/911 `/scratch/stefan/7916143/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1)=C1CC1) `REAL250005061774.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061774 none CC(C(=O)NCC(C)N(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', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 147, 147, 147, 94, 57, 29, 57, 10, 29, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 147, 94, 94, 57, 57, 57, 57, 29, 29, 29, 1, 201, 201, 201, 201] 201 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 761 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061774 none CC(C(=O)NCC(C)N(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', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 12, 44, 92, 92, 123, 123, 190, 190, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 12, 44, 44, 92, 92, 92, 92, 123, 123, 123, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 18, 19, 20] set([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]) total number of confs: 722 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061774 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061774 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061774/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061774 Building REAL250005061775 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061775' /scratch/stefan/7916143/working/building/REAL250005061775 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061775 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061775/0 /scratch/stefan/7916143/working/building/REAL250005061775 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/912 `/scratch/stefan/7916143/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061775.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061775 none CC1=CC1C(=O)NCC(C)N(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', '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, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 61, 107, 107, 135, 135, 173, 173, 177, 177, 177, 177, 177, 2, 2, 2, 1, 1, 13, 61, 61, 107, 107, 107, 107, 135, 135, 135, 177] 177 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 691 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061775 none CC1=CC1C(=O)NCC(C)N(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', '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, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 96, 96, 96, 59, 37, 20, 37, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 96, 59, 59, 37, 37, 37, 37, 20, 20, 20, 1] 177 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: 613 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061775 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061775 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061775/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061775 Building REAL250005061776 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061776' /scratch/stefan/7916143/working/building/REAL250005061776 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061776 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061776/0 /scratch/stefan/7916143/working/building/REAL250005061776 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/913 `/scratch/stefan/7916143/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C(=O)N(C)C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061776.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061776 none CC(CNC(=O)C(=O)N(C)C)N(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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 9, 11, 11, 11, 14, 14, 14, 14, 5, 6, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 11, 14, 14, 14, 14, 14, 14, 6, 6, 6, 1] 14 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061776 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061776 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061776/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061776 Building REAL250005061777 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061777' /scratch/stefan/7916143/working/building/REAL250005061777 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061777 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061777/0 /scratch/stefan/7916143/working/building/REAL250005061777 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/914 `/scratch/stefan/7916143/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)C(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061777.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061777 none CCCC(O)C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 333 conformations in input total number of sets (complete confs): 333 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 83, 70, 83, 70, 70, 44, 24, 17, 24, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 111, 83, 249, 70, 44, 44, 24, 24, 24, 24, 17, 17, 17, 1] 333 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: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061777 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061777 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061777/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061777 Building REAL250005061778 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061778' /scratch/stefan/7916143/working/building/REAL250005061778 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061778 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061778/0 /scratch/stefan/7916143/working/building/REAL250005061778 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/915 `/scratch/stefan/7916143/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061778.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061778 none CCC(O)CC(=O)NCC(C)N(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', '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, 12, 5, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 32, 35, 24, 24, 24, 15, 13, 10, 13, 6, 10, 1, 6, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 105, 32, 32, 24, 15, 15, 13, 13, 13, 13, 10, 10, 10, 1] 105 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: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061778 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061778 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061778/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061778 Building REAL250005061779 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061779' /scratch/stefan/7916143/working/building/REAL250005061779 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061779 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061779/0 /scratch/stefan/7916143/working/building/REAL250005061779 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/916 `/scratch/stefan/7916143/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)[C@H]1CC(=O)N1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061779.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061779 none CC(CNC(=O)[C@H]1CC(=O)N1)N(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.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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, 8, 1, 11, 5, 7, 5, 1, 11, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 23, 23, 30, 30, 30, 30, 30, 30, 30, 20, 20, 20, 20, 15, 15, 6, 1, 1, 1, 23, 23, 23, 30] 30 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061779 none CC(CNC(=O)[C@H]1CC(=O)N1)N(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.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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, 8, 1, 11, 5, 7, 5, 1, 11, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 16, 23, 26, 26, 26, 30, 30, 30, 30, 30, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 23, 23, 26, 30, 30, 30, 12, 12, 12, 1] 30 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: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061779 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061779 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061779/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061779 Building REAL250005061780 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061780' /scratch/stefan/7916143/working/building/REAL250005061780 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061780 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061780/0 /scratch/stefan/7916143/working/building/REAL250005061780 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/917 `/scratch/stefan/7916143/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NCC(C)N(C)C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005061780.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061780 none COC1(C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 1, 1, 13, 13, 13, 35, 59, 59, 70, 70, 90, 90, 92, 92, 92, 92, 92, 1, 1, 5, 5, 5, 13, 35, 35, 59, 59, 59, 59, 70, 70, 70, 92, 1, 1, 1, 1] 95 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: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061780 none COC1(C(=O)NCC(C)N(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', '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, 1, 11, 8, 5, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 92, 55, 55, 55, 33, 20, 13, 20, 7, 13, 1, 7, 1, 1, 1, 1, 1, 1, 92, 92, 95, 95, 95, 55, 33, 33, 20, 20, 20, 20, 13, 13, 13, 1, 92, 92, 92, 92] 95 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: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061780 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061780 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061780/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061780 Building REAL250005061781 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061781' /scratch/stefan/7916143/working/building/REAL250005061781 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061781 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061781/0 /scratch/stefan/7916143/working/building/REAL250005061781 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/918 `/scratch/stefan/7916143/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1CSC1)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061781.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061781 none CC(CNC(=O)C1CSC1)N(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.3', 'C.3', 'S.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, 8, 1, 11, 5, 5, 14, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [75, 40, 10, 10, 1, 10, 1, 1, 1, 1, 75, 88, 88, 102, 102, 104, 104, 104, 104, 104, 75, 75, 75, 75, 40, 40, 10, 1, 1, 1, 1, 1, 88, 88, 88, 104] 104 rigid atoms, others: [4, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 424 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061781 none CC(CNC(=O)C1CSC1)N(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.3', 'C.3', 'S.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, 8, 1, 11, 5, 5, 14, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 21, 32, 52, 69, 69, 69, 104, 104, 104, 7, 21, 1, 7, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 52, 52, 69, 104, 104, 104, 104, 104, 21, 21, 21, 1] 104 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 388 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061781 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061781 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061781/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061781 Building REAL250005061782 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061782' /scratch/stefan/7916143/working/building/REAL250005061782 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061782 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061782/0 /scratch/stefan/7916143/working/building/REAL250005061782 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/919 `/scratch/stefan/7916143/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005061782.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061782 none C=CC(=O)NCC(C)N(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 55, 34, 20, 34, 7, 20, 1, 7, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 55, 55, 34, 34, 34, 34, 20, 20, 20, 1] 74 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: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061782 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061782 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061782/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061782 Building REAL250005061783 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061783' /scratch/stefan/7916143/working/building/REAL250005061783 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061783 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061783/0 /scratch/stefan/7916143/working/building/REAL250005061783 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/920 `/scratch/stefan/7916143/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC(=O)N1) `REAL250005061783.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061783 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 6, 4, 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: [57, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 60, 87, 86, 112, 112, 130, 130, 130, 130, 60, 60, 60, 60, 21, 21, 4, 1, 87, 87, 87, 130, 130, 130, 130] 130 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 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: 499 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061783 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 6, 4, 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: [58, 27, 58, 97, 130, 130, 130, 130, 130, 130, 130, 130, 7, 27, 1, 7, 1, 1, 1, 1, 1, 58, 58, 58, 58, 97, 97, 130, 130, 27, 27, 27, 1, 1, 1, 1] 130 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 522 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061783 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061783 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061783/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061783 Building REAL250005061784 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061784' /scratch/stefan/7916143/working/building/REAL250005061784 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061784 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061784/0 /scratch/stefan/7916143/working/building/REAL250005061784 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/921 `/scratch/stefan/7916143/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC(F)C1) `REAL250005061784.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061784 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 15, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 64, 105, 105, 177, 177, 201, 201, 201, 201, 64, 64, 64, 64, 22, 22, 4, 1, 105, 105, 105, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 716 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061784 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1CC(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 5, 5, 5, 15, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 59, 138, 201, 201, 201, 201, 201, 201, 201, 201, 6, 24, 1, 6, 1, 1, 1, 1, 1, 59, 59, 59, 59, 138, 138, 201, 201, 24, 24, 24, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 791 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061784 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061784 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061784/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061784 Building REAL250005061785 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061785' /scratch/stefan/7916143/working/building/REAL250005061785 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061785 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061785/0 /scratch/stefan/7916143/working/building/REAL250005061785 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/922 `/scratch/stefan/7916143/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CC=NO1) `REAL250005061785.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061785 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CC=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 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: [52, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 52, 79, 79, 130, 130, 155, 155, 155, 155, 52, 52, 52, 52, 19, 19, 4, 1, 79, 79, 79, 155, 155] 155 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 477 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061785 none CC(CNC(=O)C1=CC(=O)[N-]O1)N(C)C(=O)C1=CC=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 11, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 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: [63, 32, 63, 115, 155, 155, 155, 155, 155, 155, 155, 155, 11, 32, 1, 11, 1, 1, 1, 1, 1, 63, 63, 63, 63, 115, 115, 155, 155, 32, 32, 32, 1, 1] 155 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 619 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061785 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061785 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061785/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061785 Building REAL250005061786 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061786' /scratch/stefan/7916143/working/building/REAL250005061786 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061786 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061786/0 /scratch/stefan/7916143/working/building/REAL250005061786 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/923 `/scratch/stefan/7916143/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC(CNC(=O)C1=CC(=O)[N-]O1)CC(C)C) `REAL250005061786.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061786 none CCC(=O)NC(CNC(=O)C1=CC(=O)[N-]O1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [176, 133, 133, 133, 98, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 93, 120, 122, 118, 176, 176, 176, 176, 176, 133, 98, 29, 29, 9, 1, 120, 120, 122, 122, 122, 122, 122, 122, 122] 179 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 924 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061786 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061786 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061786/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061786 Building REAL250005061787 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061787' /scratch/stefan/7916143/working/building/REAL250005061787 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061787 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061787/0 /scratch/stefan/7916143/working/building/REAL250005061787 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/924 `/scratch/stefan/7916143/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(CNC(=O)C1=CC(=O)[N-]O1)CC(C)C) `REAL250005061787.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061787 none CC(=O)NC(CNC(=O)C1=CC(=O)[N-]O1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 30, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 31, 31, 31, 31, 30, 15, 15, 6, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30] 31 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 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: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061787 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061787 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061787/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061787 Building REAL250005061788 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061788' /scratch/stefan/7916143/working/building/REAL250005061788 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061788 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061788/0 /scratch/stefan/7916143/working/building/REAL250005061788 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/925 `/scratch/stefan/7916143/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1) `REAL250005061788.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061788 none CC(C)CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [103, 102, 100, 77, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 81, 116, 116, 116, 189, 189, 103, 103, 103, 103, 103, 103, 103, 102, 102, 81, 26, 26, 8, 1, 116, 189, 189, 189, 189, 189] 190 rigid atoms, others: [34, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 824 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061788 none CC(C)CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [58, 57, 58, 41, 12, 41, 134, 187, 187, 187, 192, 192, 192, 192, 192, 12, 1, 12, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58, 57, 57, 41, 134, 134, 187, 192, 12, 1, 1, 1, 1, 1] 193 rigid atoms, others: [36, 37, 38, 39, 40, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 794 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061788 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061788 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061788/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061788 Building REAL250005061789 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061789' /scratch/stefan/7916143/working/building/REAL250005061789 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061789 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061789/0 /scratch/stefan/7916143/working/building/REAL250005061789 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/926 `/scratch/stefan/7916143/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NC(CNC(=O)C1=CC(=O)[N-]O1)CC(C)C) `REAL250005061789.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061789 none COCC(=O)NC(CNC(=O)C1=CC(=O)[N-]O1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 177, 88, 88, 88, 55, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 55, 79, 79, 79, 180, 180, 180, 178, 178, 88, 55, 19, 19, 5, 1, 79, 79, 79, 79, 79, 79, 79, 79, 79] 180 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 890 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061789 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061789 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061789/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061789 Building REAL250005061790 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061790' /scratch/stefan/7916143/working/building/REAL250005061790 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061790 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061790/0 /scratch/stefan/7916143/working/building/REAL250005061790 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/927 `/scratch/stefan/7916143/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NC(CNC(=O)C1=CC(=O)[N-]O1)CC(C)C) `REAL250005061790.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061790 none CCCC(=O)NC(CNC(=O)C1=CC(=O)[N-]O1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 119, 119, 119, 70, 22, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 67, 88, 88, 85, 201, 201, 201, 201, 201, 195, 195, 119, 70, 22, 22, 5, 1, 88, 88, 88, 88, 88, 88, 88, 88, 88] 201 rigid atoms, others: [33, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 980 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061790 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061790 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061790/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061790 Building REAL250005061791 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061791' /scratch/stefan/7916143/working/building/REAL250005061791 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061791 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061791/0 /scratch/stefan/7916143/working/building/REAL250005061791 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/928 `/scratch/stefan/7916143/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)C) `REAL250005061791.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061791 none CC(C)CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [138, 137, 134, 101, 36, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 106, 156, 156, 156, 194, 194, 138, 138, 138, 138, 138, 138, 138, 137, 137, 106, 36, 36, 9, 1, 156, 194, 194, 194, 194, 194, 194, 194] 198 rigid atoms, others: [34, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 1018 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061791 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061791 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061791/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061791 Building REAL250005061792 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061792' /scratch/stefan/7916143/working/building/REAL250005061792 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061792 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061792/0 /scratch/stefan/7916143/working/building/REAL250005061792 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/929 `/scratch/stefan/7916143/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(N)=O) `REAL250005061792.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061792 none CC(C)CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 53, 48, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 49, 59, 59, 59, 62, 62, 54, 54, 54, 54, 54, 54, 54, 54, 54, 49, 18, 18, 8, 1, 59, 62, 62] 62 rigid atoms, others: [34, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 268 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061792 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061792 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061792/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061792 Building REAL250005061793 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061793' /scratch/stefan/7916143/working/building/REAL250005061793 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061793 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061793/0 /scratch/stefan/7916143/working/building/REAL250005061793 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/930 `/scratch/stefan/7916143/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NC(CNC(=O)C1=CC(=O)[N-]O1)CC(C)C) `REAL250005061793.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061793 none C=CCC(=O)NC(CNC(=O)C1=CC(=O)[N-]O1)CC(C)C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 113, 113, 113, 66, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 65, 91, 91, 90, 201, 201, 201, 199, 199, 113, 66, 21, 21, 5, 1, 91, 91, 91, 91, 91, 91, 91, 91, 91] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 981 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061793 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061793 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061793/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061793 Building REAL250005061794 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061794' /scratch/stefan/7916143/working/building/REAL250005061794 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061794 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061794/0 /scratch/stefan/7916143/working/building/REAL250005061794 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/931 `/scratch/stefan/7916143/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CO) `REAL250005061794.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061794 none CC(C)CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 44, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 44, 57, 57, 57, 65, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 17, 17, 7, 1, 57, 65, 65, 195] 195 rigid atoms, others: [33, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 491 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061794 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061794 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061794/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061794 Building REAL250005061795 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061795' /scratch/stefan/7916143/working/building/REAL250005061795 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061795 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061795/0 /scratch/stefan/7916143/working/building/REAL250005061795 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/932 `/scratch/stefan/7916143/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)O) `REAL250005061795.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061795 none CC(C)CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 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] 1 hydrogens need rotated 252 conformations in input total number of sets (complete confs): 252 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 43, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 43, 63, 63, 63, 84, 84, 52, 52, 52, 52, 52, 52, 52, 52, 52, 43, 17, 17, 5, 1, 63, 84, 84, 84, 84, 252] 252 rigid atoms, others: [34, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 661 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061795 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061795 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061795/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061795 Building REAL250005061796 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061796' /scratch/stefan/7916143/working/building/REAL250005061796 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061796 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061796/0 /scratch/stefan/7916143/working/building/REAL250005061796 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/933 `/scratch/stefan/7916143/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H](C)O) `REAL250005061796.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061796 none CC(C)CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 285 conformations in input total number of sets (complete confs): 285 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 50, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 50, 75, 75, 75, 95, 95, 95, 63, 63, 63, 63, 63, 63, 63, 63, 63, 50, 17, 17, 5, 1, 75, 95, 95, 95, 285] 285 rigid atoms, others: [35, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 750 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061796 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061796 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061796/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061796 Building REAL250005061797 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061797' /scratch/stefan/7916143/working/building/REAL250005061797 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061797 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061797/0 /scratch/stefan/7916143/working/building/REAL250005061797 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/934 `/scratch/stefan/7916143/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](C)O) `REAL250005061797.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061797 none CC(C)CC(CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 483 conformations in input total number of sets (complete confs): 483 using faster count positions algorithm for large data unique positions, atoms: [80, 83, 84, 59, 29, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 59, 97, 97, 97, 157, 157, 157, 84, 84, 84, 84, 84, 84, 84, 83, 83, 59, 29, 29, 10, 1, 97, 157, 157, 157, 471] 483 rigid atoms, others: [35, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 1293 number of broken/clashed sets: 153 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061797 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061797 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061797/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061797 Building REAL250005061798 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061798' /scratch/stefan/7916143/working/building/REAL250005061798 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061798 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061798/0 /scratch/stefan/7916143/working/building/REAL250005061798 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/935 `/scratch/stefan/7916143/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NC(CNC(=O)C1=CC(=O)[N-]O1)CC(C)C) `REAL250005061798.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061798 none CC=CC(=O)NC(CNC(=O)C1=CC(=O)[N-]O1)CC(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.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, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 61, 61, 61, 53, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 52, 55, 55, 55, 80, 80, 80, 80, 80, 61, 53, 19, 19, 8, 1, 55, 55, 55, 55, 55, 55, 55, 55, 55] 80 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 316 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061798 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061798 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061798/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061798 Building REAL250005061799 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061799' /scratch/stefan/7916143/working/building/REAL250005061799 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061799 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061799/0 /scratch/stefan/7916143/working/building/REAL250005061799 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/936 `/scratch/stefan/7916143/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061799.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061799 none COCC(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 178, 83, 83, 83, 37, 14, 6, 14, 29, 30, 30, 6, 1, 6, 1, 1, 1, 1, 1, 1, 187, 187, 187, 178, 178, 83, 37, 37, 14, 29, 29, 30, 30, 30, 30, 30, 30, 30, 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: 792 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061799 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061799 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061799/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061799 Building REAL250005061800 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061800' /scratch/stefan/7916143/working/building/REAL250005061800 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061800 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061800/0 /scratch/stefan/7916143/working/building/REAL250005061800 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/937 `/scratch/stefan/7916143/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061800.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061800 none CCCC(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 175, 91, 91, 91, 37, 15, 4, 15, 30, 31, 31, 4, 1, 4, 1, 1, 1, 1, 1, 1, 182, 182, 182, 182, 182, 175, 175, 91, 37, 37, 15, 30, 30, 31, 31, 31, 31, 31, 31, 31, 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: 819 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061800 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061800 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061800/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061800 Building REAL250005061801 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061801' /scratch/stefan/7916143/working/building/REAL250005061801 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061801 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061801/0 /scratch/stefan/7916143/working/building/REAL250005061801 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/938 `/scratch/stefan/7916143/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CNC(=O)C(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061801.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061801 none CC(C)CC(CNC(=O)C(C)C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 51, 23, 9, 23, 71, 136, 136, 136, 188, 188, 9, 1, 9, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 49, 49, 23, 71, 71, 136, 188, 188, 188, 188, 188, 188, 188, 9, 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: 891 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061801 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061801 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061801/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061801 Building REAL250005061802 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061802' /scratch/stefan/7916143/working/building/REAL250005061802 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061802 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061802/0 /scratch/stefan/7916143/working/building/REAL250005061802 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/939 `/scratch/stefan/7916143/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061802.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061802 none CCC(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [184, 137, 137, 137, 76, 29, 9, 29, 54, 56, 56, 9, 1, 9, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 184, 137, 76, 76, 29, 54, 54, 56, 56, 56, 56, 56, 56, 56, 9, 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: 876 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061802 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061802 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061802/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061802 Building REAL250005061803 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061803' /scratch/stefan/7916143/working/building/REAL250005061803 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061803 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061803/0 /scratch/stefan/7916143/working/building/REAL250005061803 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/940 `/scratch/stefan/7916143/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061803.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061803 none CC(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 36, 17, 9, 17, 28, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 36, 36, 17, 28, 28, 29, 29, 29, 29, 29, 29, 29, 9, 1] 48 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: 223 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061803 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061803 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061803/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061803 Building REAL250005061804 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061804' /scratch/stefan/7916143/working/building/REAL250005061804 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061804 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061804/0 /scratch/stefan/7916143/working/building/REAL250005061804 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/941 `/scratch/stefan/7916143/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CNC(=O)C1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061804.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061804 none CC(C)CC(CNC(=O)C1CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 168, 173, 128, 58, 12, 12, 1, 12, 1, 1, 1, 128, 169, 169, 169, 182, 182, 182, 182, 182, 173, 173, 173, 173, 173, 173, 173, 168, 168, 128, 58, 58, 12, 1, 1, 1, 1, 1, 169, 182] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 955 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061804 none CC(C)CC(CNC(=O)C1CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 42, 43, 19, 7, 19, 53, 107, 107, 107, 182, 182, 7, 1, 7, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 42, 42, 19, 53, 53, 107, 182, 182, 182, 182, 182, 7, 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: 727 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061804 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061804 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061804/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061804 Building REAL250005061805 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061805' /scratch/stefan/7916143/working/building/REAL250005061805 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061805 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061805/0 /scratch/stefan/7916143/working/building/REAL250005061805 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/942 `/scratch/stefan/7916143/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CNC(=O)C(N)=O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061805.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061805 none CC(C)CC(CNC(=O)C(N)=O)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 6, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 20, 9, 20, 47, 86, 86, 86, 94, 94, 9, 1, 9, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 47, 47, 86, 94, 94, 9, 1] 103 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: 412 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061805 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061805 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061805/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061805 Building REAL250005061806 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061806' /scratch/stefan/7916143/working/building/REAL250005061806 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061806 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061806/0 /scratch/stefan/7916143/working/building/REAL250005061806 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/943 `/scratch/stefan/7916143/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CNC(=O)CO)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061806.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061806 none CC(C)CC(CNC(=O)CO)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 363 conformations in input total number of sets (complete confs): 363 using faster count positions algorithm for large data unique positions, atoms: [39, 38, 39, 21, 8, 21, 46, 85, 85, 85, 113, 8, 1, 8, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 38, 38, 21, 46, 46, 85, 114, 114, 342, 8, 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: 892 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061806 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061806 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061806/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061806 Building REAL250005061807 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061807' /scratch/stefan/7916143/working/building/REAL250005061807 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061807 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061807/0 /scratch/stefan/7916143/working/building/REAL250005061807 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/944 `/scratch/stefan/7916143/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CNC(=O)C(C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061807.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061807 none CC(C)CC(CNC(=O)C(C)O)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 525 conformations in input total number of sets (complete confs): 525 using faster count positions algorithm for large data unique positions, atoms: [38, 37, 38, 21, 8, 21, 48, 102, 102, 102, 161, 161, 8, 1, 8, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 37, 37, 21, 48, 48, 102, 161, 161, 161, 161, 483, 8, 1] 525 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: 1197 number of broken/clashed sets: 159 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061807 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061807 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061807/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061807 Building REAL250005061808 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061808' /scratch/stefan/7916143/working/building/REAL250005061808 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061808 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061808/0 /scratch/stefan/7916143/working/building/REAL250005061808 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/945 `/scratch/stefan/7916143/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061808.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061808 none CC(=O)C(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [112, 102, 112, 102, 102, 58, 25, 9, 25, 44, 44, 44, 9, 1, 9, 1, 1, 1, 1, 1, 1, 112, 112, 112, 102, 58, 58, 25, 44, 44, 44, 44, 44, 44, 44, 44, 44, 9, 1] 129 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: 501 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061808 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061808 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061808/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061808 Building REAL250005061809 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061809' /scratch/stefan/7916143/working/building/REAL250005061809 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061809 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061809/0 /scratch/stefan/7916143/working/building/REAL250005061809 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/946 `/scratch/stefan/7916143/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061809.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061809 none CC=CC(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 78, 78, 78, 45, 22, 10, 22, 38, 38, 38, 10, 1, 10, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 78, 45, 45, 22, 38, 38, 38, 38, 38, 38, 38, 38, 38, 10, 1] 119 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 461 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061809 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061809 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061809/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061809 Building REAL250005061810 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061810' /scratch/stefan/7916143/working/building/REAL250005061810 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061810 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061810/0 /scratch/stefan/7916143/working/building/REAL250005061810 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/947 `/scratch/stefan/7916143/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CNC(=O)[C@H](C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061810.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061810 none CC(C)CC(CNC(=O)[C@H](C)O)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 249 conformations in input total number of sets (complete confs): 249 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 13, 8, 13, 30, 61, 61, 61, 83, 83, 83, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 30, 30, 61, 83, 83, 83, 249, 8, 1] 249 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: 609 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061810 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061810 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061810/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061810 Building REAL250005061811 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061811' /scratch/stefan/7916143/working/building/REAL250005061811 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061811 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061811/0 /scratch/stefan/7916143/working/building/REAL250005061811 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/948 `/scratch/stefan/7916143/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061811.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061811 none C=CCC(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 184, 87, 87, 87, 35, 15, 5, 15, 28, 29, 29, 5, 1, 5, 1, 1, 1, 1, 1, 1, 189, 189, 189, 184, 184, 87, 35, 35, 15, 28, 28, 29, 29, 29, 29, 29, 29, 29, 5, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 803 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061811 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061811 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061811/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061811 Building REAL250005061812 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061812' /scratch/stefan/7916143/working/building/REAL250005061812 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061812 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061812/0 /scratch/stefan/7916143/working/building/REAL250005061812 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/949 `/scratch/stefan/7916143/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CNC(=O)CC#N)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061812.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061812 none CC(C)CC(CNC(=O)CC#N)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 40, 41, 19, 9, 19, 52, 106, 106, 106, 173, 173, 9, 1, 9, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 40, 40, 19, 52, 52, 106, 173, 173, 9, 1] 201 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 786 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061812 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061812 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061812/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061812 Building REAL250005061813 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061813' /scratch/stefan/7916143/working/building/REAL250005061813 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061813 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061813/0 /scratch/stefan/7916143/working/building/REAL250005061813 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/950 `/scratch/stefan/7916143/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CNC(=O)[C@@H](C)O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061813.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061813 none CC(C)CC(CNC(=O)[C@@H](C)O)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 273 conformations in input total number of sets (complete confs): 273 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 15, 9, 15, 34, 71, 71, 71, 91, 91, 91, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 34, 34, 71, 91, 91, 91, 273, 9, 1] 273 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: 673 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061813 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061813 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061813/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061813 Building REAL250005061814 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061814' /scratch/stefan/7916143/working/building/REAL250005061814 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061814 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061814/0 /scratch/stefan/7916143/working/building/REAL250005061814 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/951 `/scratch/stefan/7916143/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061814.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061814 none C=CC(=O)NCC(CC(C)C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [118, 100, 100, 100, 65, 24, 8, 24, 53, 55, 55, 8, 1, 8, 1, 1, 1, 1, 1, 1, 118, 118, 118, 100, 65, 65, 24, 53, 53, 55, 55, 55, 55, 55, 55, 55, 8, 1] 127 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: 615 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061814 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061814 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061814/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061814 Building REAL250005061815 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061815' /scratch/stefan/7916143/working/building/REAL250005061815 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061815 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061815/0 /scratch/stefan/7916143/working/building/REAL250005061815 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/952 `/scratch/stefan/7916143/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(CNC(=O)C1=CC(=O)[N-]O1)C1CCCCC1) `REAL250005061815.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061815 none CC(=O)NC(CNC(=O)C1=CC(=O)[N-]O1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 45, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 44, 63, 63, 61, 63, 63, 52, 52, 52, 52, 45, 22, 22, 9, 1, 62, 63, 63, 63, 63, 61, 63, 63, 63, 63, 63] 65 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 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: 262 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061815 none CC(=O)NC(CNC(=O)C1=CC(=O)[N-]O1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 9, 1, 9, 22, 53, 53, 53, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 9, 22, 22, 53, 63, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 65 rigid atoms, others: [32, 33, 34, 35, 4, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 36, 30, 31] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 232 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061815 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061815 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061815/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061815 Building REAL250005061816 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061816' /scratch/stefan/7916143/working/building/REAL250005061816 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061816 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061816/0 /scratch/stefan/7916143/working/building/REAL250005061816 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/953 `/scratch/stefan/7916143/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C1CCCCC1) `REAL250005061816.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061816 none CC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 33, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 29, 30, 30, 30, 30, 43, 43, 43, 43, 33, 33, 13, 7, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 48 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 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: 222 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061816 none CC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 21, 7, 1, 7, 17, 17, 17, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 21, 21, 7, 17, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 48 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 39, 40, 15, 16, 17, 18, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 187 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061816 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061816 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061816/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061816 Building REAL250005061817 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061817' /scratch/stefan/7916143/working/building/REAL250005061817 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061817 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061817/0 /scratch/stefan/7916143/working/building/REAL250005061817 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/954 `/scratch/stefan/7916143/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1) `REAL250005061817.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061817 none CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 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] 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: [11, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 1, 1, 1, 12, 12, 12, 12, 11, 1, 1, 1, 1, 1, 6, 8, 1, 2, 2, 2, 1, 1] 24 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 37, 17, 18, 19, 25, 26, 27, 28, 29, 36] set([0, 1, 34, 3, 33, 9, 10, 11, 12, 13, 14, 15, 16, 35, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061817 none CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 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] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 8, 24, 8, 8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 5, 1, 8, 8, 8, 8, 8, 8] 24 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061817 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061817 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061817/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061817 Building REAL250005061818 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061818' /scratch/stefan/7916143/working/building/REAL250005061818 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061818 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061818/0 /scratch/stefan/7916143/working/building/REAL250005061818 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/955 `/scratch/stefan/7916143/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1) `REAL250005061818.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061818 none CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [5, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 6, 9, 1, 2, 2, 2, 1, 1] 13 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 33, 16, 17, 18, 22, 23, 24, 25, 26, 29] set([0, 32, 2, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 27, 28, 30, 31]) total number of confs: 33 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061818 none CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 9, 13, 9, 9, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 13, 9, 9, 9, 9, 9, 7, 1, 9, 9, 9, 9, 9, 9] 13 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 37 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061818 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061818 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061818/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061818 Building REAL250005061819 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061819' /scratch/stefan/7916143/working/building/REAL250005061819 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061819 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061819/0 /scratch/stefan/7916143/working/building/REAL250005061819 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/956 `/scratch/stefan/7916143/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(C(=O)C2CC2)CCC1NC(=O)C1=CC(=O)[N-]O1) `REAL250005061819.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061819 none CC1CN(C(=O)C2CC2)CCC1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 13, 13, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 5, 9] 30 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 9, 10, 11, 12, 34, 35, 24, 25, 26, 36] set([5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061819 none CC1CN(C(=O)C2CC2)CCC1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 8, 1, 8, 1, 1, 1, 13, 13, 13, 13, 26, 26, 26, 30, 30, 30, 30, 30, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 26, 30] 30 rigid atoms, others: [4, 6, 7, 8, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005061819 none CC1CN(C(=O)C2CC2)CCC1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 9, 9, 9, 19, 19, 30, 30, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 9, 9, 9, 9, 9, 6, 1] 30 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: 101 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061819 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061819 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061819/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061819 Building REAL250005061820 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061820' /scratch/stefan/7916143/working/building/REAL250005061820 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061820 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061820/0 /scratch/stefan/7916143/working/building/REAL250005061820 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/957 `/scratch/stefan/7916143/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1) `REAL250005061820.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061820 none COCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 18, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 1, 1, 38, 39, 39, 19, 18, 1, 1, 1, 1, 1, 6, 13, 1, 2, 2, 2, 1, 1] 50 rigid atoms, others: [33, 3, 5, 6, 7, 8, 9, 38, 18, 19, 20, 26, 27, 28, 29, 30, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 31, 32, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061820 none COCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 34, 13, 34, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 50, 50, 50, 48, 48, 13, 13, 13, 13, 13, 7, 1, 13, 13, 13, 13, 13, 13] 50 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: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061820 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061820 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061820/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061820 Building REAL250005061821 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061821' /scratch/stefan/7916143/working/building/REAL250005061821 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061821 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061821/0 /scratch/stefan/7916143/working/building/REAL250005061821 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/958 `/scratch/stefan/7916143/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1) `REAL250005061821.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061821 none CCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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: [28, 20, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 1, 1, 29, 29, 29, 28, 28, 20, 20, 1, 1, 1, 1, 1, 6, 13, 1, 2, 2, 2, 1, 1] 47 rigid atoms, others: [32, 35, 3, 5, 6, 7, 8, 9, 39, 40, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 33, 34, 36, 37, 38]) total number of confs: 156 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061821 none CCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 34, 13, 34, 13, 13, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 47, 47, 47, 47, 47, 47, 47, 13, 13, 13, 13, 13, 6, 1, 13, 13, 13, 13, 13, 13] 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: 165 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061821 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061821 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061821/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061821 Building REAL250005061822 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061822' /scratch/stefan/7916143/working/building/REAL250005061822 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061822 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061822/0 /scratch/stefan/7916143/working/building/REAL250005061822 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/959 `/scratch/stefan/7916143/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1) `REAL250005061822.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061822 none CC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 6, 11, 1, 2, 2, 2, 1, 1] 31 rigid atoms, others: [32, 35, 3, 5, 6, 7, 8, 9, 39, 40, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 33, 34, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061822 none CC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 11, 31, 11, 11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 11, 11, 11, 11, 11, 7, 1, 11, 11, 11, 11, 11, 11] 31 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: 83 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061822 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061822 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061822/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061822 Building REAL250005061823 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061823' /scratch/stefan/7916143/working/building/REAL250005061823 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061823 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061823/0 /scratch/stefan/7916143/working/building/REAL250005061823 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/960 `/scratch/stefan/7916143/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(C(=O)C(N)=O)CCC1NC(=O)C1=CC(=O)[N-]O1) `REAL250005061823.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061823 none CC1CN(C(=O)C(N)=O)CCC1NC(=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', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 11, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 17, 17, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 17, 17, 1, 1, 1, 1, 1, 6, 11] 30 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 9, 10, 11, 12, 24, 25, 26, 29, 30, 31] set([34, 35, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061823 none CC1CN(C(=O)C(N)=O)CCC1NC(=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', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 11, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 22, 22, 30, 30, 11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 30, 30, 11, 11, 11, 11, 11, 6, 1] 30 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: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061823 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061823 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061823/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061823 Building REAL250005061824 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061824' /scratch/stefan/7916143/working/building/REAL250005061824 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061824 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061824/0 /scratch/stefan/7916143/working/building/REAL250005061824 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/961 `/scratch/stefan/7916143/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1) `REAL250005061824.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061824 none C=CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.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, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [47, 22, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 47, 47, 47, 23, 22, 1, 1, 1, 1, 1, 6, 18, 1, 2, 2, 2, 1, 1] 64 rigid atoms, others: [33, 3, 5, 6, 7, 8, 9, 38, 18, 19, 20, 26, 27, 28, 29, 30, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 31, 32, 34, 35, 36]) total number of confs: 198 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061824 none C=CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.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, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 47, 18, 47, 18, 18, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 64, 64, 64, 64, 64, 18, 18, 18, 18, 18, 8, 1, 18, 18, 18, 18, 18, 18] 64 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: 222 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061824 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061824 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061824/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061824 Building REAL250005061825 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061825' /scratch/stefan/7916143/working/building/REAL250005061825 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061825 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061825/0 /scratch/stefan/7916143/working/building/REAL250005061825 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/962 `/scratch/stefan/7916143/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(C(=O)CO)CCC1NC(=O)C1=CC(=O)[N-]O1) `REAL250005061825.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061825 none CC1CN(C(=O)CO)CCC1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 20, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 1, 21, 21, 60, 1, 1, 1, 1, 1, 6, 14] 93 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 23, 24, 25, 29, 30, 31] set([34, 35, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28]) total number of confs: 164 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061825 none CC1CN(C(=O)CO)CCC1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 31, 31, 31, 14, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 31, 31, 93, 14, 14, 14, 14, 14, 8, 1] 93 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: 184 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061825 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061825 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061825/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061825 Building REAL250005061826 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061826' /scratch/stefan/7916143/working/building/REAL250005061826 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061826 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061826/0 /scratch/stefan/7916143/working/building/REAL250005061826 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/963 `/scratch/stefan/7916143/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1) `REAL250005061826.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061826 none CC(O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 1, 1, 1, 16, 16, 16, 16, 48, 1, 1, 1, 1, 1, 6, 9, 1, 2, 2, 2, 1, 1] 66 rigid atoms, others: [33, 3, 5, 6, 7, 8, 9, 38, 18, 19, 20, 26, 27, 28, 29, 30, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 31, 32, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061826 none CC(O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [22, 20, 22, 9, 20, 9, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 22, 22, 22, 22, 66, 9, 9, 9, 9, 9, 6, 1, 9, 9, 9, 9, 9, 9] 66 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: 135 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061826 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061826 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061826/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061826 Building REAL250005061827 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061827' /scratch/stefan/7916143/working/building/REAL250005061827 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061827 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061827/0 /scratch/stefan/7916143/working/building/REAL250005061827 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/964 `/scratch/stefan/7916143/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(C(=O)CCF)CCC1NC(=O)C1=CC(=O)[N-]O1) `REAL250005061827.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061827 none CC1CN(C(=O)CCF)CCC1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 5, 5, 15, 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, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 16, 25, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 17, 17, 25, 25, 1, 1, 1, 1, 1, 6, 11] 40 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 9, 10, 11, 12, 34, 35, 24, 25, 26, 31] set([36, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 37]) total number of confs: 144 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061827 none CC1CN(C(=O)CCF)CCC1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 5, 5, 15, 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, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 11, 11, 28, 28, 40, 40, 11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 40, 40, 40, 40, 11, 11, 11, 11, 11, 5, 1] 40 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: 145 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061827 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061827 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061827/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061827 Building REAL250005061828 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061828' /scratch/stefan/7916143/working/building/REAL250005061828 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061828 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061828/0 /scratch/stefan/7916143/working/building/REAL250005061828 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/965 `/scratch/stefan/7916143/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1) `REAL250005061828.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061828 none C[C@@H](O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.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'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [16, 7, 16, 16, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 1, 1, 1, 16, 16, 16, 48, 1, 1, 1, 1, 1, 5, 9, 1, 2, 2, 2, 1, 1] 69 rigid atoms, others: [33, 4, 37, 6, 7, 8, 9, 10, 38, 19, 20, 21, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 31, 32, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061828 none C[C@@H](O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.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'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 21, 23, 23, 9, 21, 9, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 69, 9, 9, 9, 9, 9, 5, 1, 9, 9, 9, 9, 9, 9] 69 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 138 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061828 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061828 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061828/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061828 Building REAL250005061829 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061829' /scratch/stefan/7916143/working/building/REAL250005061829 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061829 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061829/0 /scratch/stefan/7916143/working/building/REAL250005061829 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/966 `/scratch/stefan/7916143/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1) `REAL250005061829.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061829 none C[C@H](O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.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'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 15, 15, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 1, 1, 1, 15, 15, 15, 45, 1, 1, 1, 1, 1, 6, 9, 1, 2, 2, 2, 1, 1] 63 rigid atoms, others: [33, 4, 37, 6, 7, 8, 9, 10, 38, 19, 20, 21, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 31, 32, 34, 35, 36]) total number of confs: 122 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061829 none C[C@H](O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.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'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [21, 19, 21, 21, 9, 19, 9, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 63, 9, 9, 9, 9, 9, 5, 1, 9, 9, 9, 9, 9, 9] 63 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 128 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061829 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061829 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061829/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061829 Building REAL250005061830 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061830' /scratch/stefan/7916143/working/building/REAL250005061830 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061830 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061830/0 /scratch/stefan/7916143/working/building/REAL250005061830 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/967 `/scratch/stefan/7916143/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1) `REAL250005061830.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061830 none CC=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 6, 16, 1, 2, 2, 2, 1, 1] 34 rigid atoms, others: [33, 3, 5, 6, 7, 8, 9, 38, 18, 19, 20, 26, 27, 28, 29, 30, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 31, 32, 34, 35, 36]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061830 none CC=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 31, 16, 31, 16, 16, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 34, 34, 34, 34, 34, 16, 16, 16, 16, 16, 9, 1, 16, 16, 16, 16, 16, 16] 34 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: 103 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061830 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061830 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061830/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061830 Building REAL250005061831 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061831' /scratch/stefan/7916143/working/building/REAL250005061831 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061831 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061831/0 /scratch/stefan/7916143/working/building/REAL250005061831 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/968 `/scratch/stefan/7916143/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C) `REAL250005061831.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061831 none COCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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, 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, 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: [50, 29, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 41, 41, 1, 1, 1, 50, 50, 50, 29, 29, 5, 1, 1, 1, 1, 1, 41, 1, 1, 1, 2, 2, 2] 116 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 32, 36, 37, 38]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061831 none COCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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, 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, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 76, 76, 76, 41, 41, 41, 41, 11, 1, 11, 1, 1, 1, 1, 1, 1, 41, 41, 41, 116, 116, 116, 116, 116, 76, 41, 41, 41, 41, 41, 1, 41, 41, 41, 41, 41, 41] 116 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: 387 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061831 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061831 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061831/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061831 Building REAL250005061832 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061832' /scratch/stefan/7916143/working/building/REAL250005061832 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061832 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061832/0 /scratch/stefan/7916143/working/building/REAL250005061832 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/969 `/scratch/stefan/7916143/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C) `REAL250005061832.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061832 none CCCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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, 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, 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: [50, 34, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 43, 43, 43, 43, 43, 1, 1, 1, 58, 58, 58, 58, 58, 34, 34, 5, 1, 1, 1, 1, 1, 43, 1, 1, 1, 2, 2, 2] 170 rigid atoms, others: [32, 33, 35, 36, 5, 6, 7, 8, 9, 10, 18, 19, 20, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 34, 38, 39, 40]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061832 none CCCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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, 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, 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, 168, 90, 90, 90, 43, 43, 43, 43, 11, 1, 11, 1, 1, 1, 1, 1, 1, 43, 43, 43, 170, 170, 170, 170, 170, 168, 168, 90, 43, 43, 43, 43, 43, 1, 43, 43, 43, 43, 43, 43] 170 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: 599 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061832 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061832 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061832/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061832 Building REAL250005061833 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061833' /scratch/stefan/7916143/working/building/REAL250005061833 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061833 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061833/0 /scratch/stefan/7916143/working/building/REAL250005061833 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/970 `/scratch/stefan/7916143/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C) `REAL250005061833.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061833 none CC(C)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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, 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, 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: [25, 6, 25, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 43, 43, 43, 43, 43, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 1, 43, 1, 1, 1, 2, 2, 2] 81 rigid atoms, others: [32, 33, 35, 36, 5, 6, 7, 8, 9, 10, 18, 19, 20, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 34, 38, 39, 40]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061833 none CC(C)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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, 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, 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, 74, 81, 74, 74, 43, 43, 43, 43, 11, 1, 11, 1, 1, 1, 1, 1, 1, 43, 43, 43, 81, 81, 81, 81, 81, 81, 81, 74, 43, 43, 43, 43, 43, 1, 43, 43, 43, 43, 43, 43] 81 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: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061833 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061833 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061833/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061833 Building REAL250005061834 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061834' /scratch/stefan/7916143/working/building/REAL250005061834 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061834 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061834/0 /scratch/stefan/7916143/working/building/REAL250005061834 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/971 `/scratch/stefan/7916143/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C) `REAL250005061834.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061834 none CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 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, 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: [33, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 1, 33, 33, 33, 33, 33, 5, 1, 1, 1, 1, 1, 36, 1, 1, 1, 2, 2, 2] 73 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 17, 18, 19, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 36, 37, 10, 11, 12, 13, 14, 15, 16, 35, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061834 none CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 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, 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, 59, 59, 59, 36, 36, 36, 36, 10, 1, 10, 1, 1, 1, 1, 1, 1, 36, 36, 36, 73, 73, 73, 73, 73, 59, 36, 36, 36, 36, 36, 1, 36, 36, 36, 36, 36, 36] 73 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 226 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061834 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061834 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061834/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061834 Building REAL250005061835 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061835' /scratch/stefan/7916143/working/building/REAL250005061835 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061835 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061835/0 /scratch/stefan/7916143/working/building/REAL250005061835 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/972 `/scratch/stefan/7916143/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C) `REAL250005061835.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061835 none CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 24, 1, 1, 1, 2, 2, 2] 26 rigid atoms, others: [3, 4, 5, 6, 7, 8, 16, 17, 18, 23, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 34, 33, 32, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 28]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061835 none CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 24, 24, 24, 24, 11, 1, 11, 1, 1, 1, 1, 1, 1, 24, 24, 24, 26, 26, 26, 26, 24, 24, 24, 24, 24, 1, 24, 24, 24, 24, 24, 24] 26 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061835 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061835 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061835/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061835 Building REAL250005061836 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061836' /scratch/stefan/7916143/working/building/REAL250005061836 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061836 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061836/0 /scratch/stefan/7916143/working/building/REAL250005061836 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/973 `/scratch/stefan/7916143/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)C1CC1) `REAL250005061836.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061836 none CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 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, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 33, 33, 33, 33, 33, 1, 1, 1, 1, 5, 5, 5, 30, 30, 2, 2, 2, 1, 1, 1, 33, 1, 1, 1, 1, 1, 5, 30, 30, 30, 30, 30] 97 rigid atoms, others: [0, 1, 2, 3, 4, 32, 12, 13, 14, 15, 24, 25, 26, 28, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 27, 33, 34, 35, 36, 37, 38]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061836 none CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 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, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 11, 1, 11, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 47, 47, 47, 97, 97, 33, 33, 33, 33, 33, 33, 1, 33, 33, 33, 33, 33, 47, 97, 97, 97, 97, 97] 97 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 256 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005061836 none CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 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, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 71, 71, 97, 97, 97, 97, 97, 29, 29, 11, 11, 1, 11, 1, 1, 1, 29, 29, 29, 29, 29, 29, 97, 29, 29, 29, 29, 29, 11, 1, 1, 1, 1, 1] 97 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: 245 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061836 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061836 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061836/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061836 Building REAL250005061837 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061837' /scratch/stefan/7916143/working/building/REAL250005061837 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061837 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061837/0 /scratch/stefan/7916143/working/building/REAL250005061837 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/974 `/scratch/stefan/7916143/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)C(N)=O) `REAL250005061837.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061837 none CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 1, 1, 5, 5, 5, 18, 18, 2, 2, 2, 1, 1, 1, 25, 1, 1, 1, 1, 1, 5, 18, 18] 55 rigid atoms, others: [0, 1, 2, 3, 4, 32, 12, 13, 14, 15, 24, 25, 26, 28, 29, 30, 31] set([33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 27]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061837 none CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 46, 46, 55, 55, 25, 25, 25, 25, 25, 25, 1, 25, 25, 25, 25, 25, 46, 55, 55] 55 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061837 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061837 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061837/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061837 Building REAL250005061838 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061838' /scratch/stefan/7916143/working/building/REAL250005061838 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061838 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061838/0 /scratch/stefan/7916143/working/building/REAL250005061838 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/975 `/scratch/stefan/7916143/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)CO) `REAL250005061838.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061838 none CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 7, 7, 32, 32, 32, 32, 32, 1, 1, 1, 1, 5, 5, 5, 24, 2, 2, 2, 1, 1, 1, 32, 1, 1, 1, 1, 1, 5, 24, 24, 72] 141 rigid atoms, others: [0, 1, 2, 3, 4, 12, 13, 14, 15, 23, 24, 25, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 26]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061838 none CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 46, 46, 46, 47, 32, 32, 32, 32, 32, 32, 1, 32, 32, 32, 32, 32, 46, 47, 47, 141] 141 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 26] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061838 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061838 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061838/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061838 Building REAL250005061839 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061839' /scratch/stefan/7916143/working/building/REAL250005061839 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061839 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061839/0 /scratch/stefan/7916143/working/building/REAL250005061839 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/976 `/scratch/stefan/7916143/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C) `REAL250005061839.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061839 none CC(O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 213 conformations in input total number of sets (complete confs): 213 using faster count positions algorithm for large data unique positions, atoms: [26, 6, 26, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 32, 1, 1, 1, 26, 26, 26, 26, 78, 6, 1, 1, 1, 1, 1, 32, 1, 1, 1, 2, 2, 2] 213 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 32, 36, 37, 38]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061839 none CC(O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 213 conformations in input total number of sets (complete confs): 213 using faster count positions algorithm for large data unique positions, atoms: [71, 51, 71, 51, 51, 32, 32, 32, 32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 32, 32, 32, 71, 71, 71, 71, 213, 51, 32, 32, 32, 32, 32, 1, 32, 32, 32, 32, 32, 32] 213 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: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061839 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061839 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061839/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061839 Building REAL250005061840 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061840' /scratch/stefan/7916143/working/building/REAL250005061840 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061840 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061840/0 /scratch/stefan/7916143/working/building/REAL250005061840 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/977 `/scratch/stefan/7916143/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C) `REAL250005061840.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061840 none CC(=O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 5, 22, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 1, 22, 22, 22, 5, 1, 1, 1, 1, 1, 29, 1, 1, 1, 2, 2, 2] 67 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 18, 19, 20, 25, 26, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 35, 21, 22, 23, 24, 36, 34, 30]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061840 none CC(=O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 52, 67, 52, 52, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 67, 67, 67, 52, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29, 29, 29] 67 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: 178 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061840 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061840 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061840/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061840 Building REAL250005061841 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061841' /scratch/stefan/7916143/working/building/REAL250005061841 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061841 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061841/0 /scratch/stefan/7916143/working/building/REAL250005061841 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/978 `/scratch/stefan/7916143/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C) `REAL250005061841.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061841 none CC=CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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, 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, 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: [24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 32, 1, 1, 1, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 32, 1, 1, 1, 2, 2, 2] 60 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 32, 36, 37, 38]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061841 none CC=CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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, 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, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 49, 49, 49, 32, 32, 32, 32, 11, 1, 11, 1, 1, 1, 1, 1, 1, 32, 32, 32, 60, 60, 60, 60, 60, 49, 32, 32, 32, 32, 32, 1, 32, 32, 32, 32, 32, 32] 60 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: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061841 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061841 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061841/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061841 Building REAL250005061842 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061842' /scratch/stefan/7916143/working/building/REAL250005061842 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061842 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061842/0 /scratch/stefan/7916143/working/building/REAL250005061842 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/979 `/scratch/stefan/7916143/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C) `REAL250005061842.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061842 none C[C@H](O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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: [28, 5, 28, 28, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 41, 41, 1, 1, 1, 28, 28, 28, 84, 5, 1, 1, 1, 1, 1, 41, 1, 1, 1, 2, 2, 2] 243 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 32, 36, 37, 38]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061842 none C[C@H](O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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, 61, 81, 81, 61, 61, 41, 41, 41, 41, 12, 1, 12, 1, 1, 1, 1, 1, 1, 41, 41, 41, 81, 81, 81, 243, 61, 41, 41, 41, 41, 41, 1, 41, 41, 41, 41, 41, 41] 243 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 484 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061842 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061842 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061842/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061842 Building REAL250005061843 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061843' /scratch/stefan/7916143/working/building/REAL250005061843 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061843 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061843/0 /scratch/stefan/7916143/working/building/REAL250005061843 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/980 `/scratch/stefan/7916143/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C) `REAL250005061843.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061843 none C=CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [66, 38, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 39, 39, 39, 39, 39, 1, 1, 1, 66, 65, 66, 38, 38, 5, 1, 1, 1, 1, 1, 39, 1, 1, 1, 2, 2, 2] 140 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 32, 36, 37, 38]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061843 none C=CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 76, 76, 76, 39, 39, 39, 39, 11, 1, 11, 1, 1, 1, 1, 1, 1, 39, 39, 39, 140, 140, 140, 140, 140, 76, 39, 39, 39, 39, 39, 1, 39, 39, 39, 39, 39, 39] 140 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: 497 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061843 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061843 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061843/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061843 Building REAL250005061844 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061844' /scratch/stefan/7916143/working/building/REAL250005061844 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061844 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061844/0 /scratch/stefan/7916143/working/building/REAL250005061844 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/981 `/scratch/stefan/7916143/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)CC#N) `REAL250005061844.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061844 none CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)CC#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 1, 1, 5, 5, 5, 38, 38, 2, 2, 2, 1, 1, 1, 33, 1, 1, 1, 1, 1, 5, 38, 38] 122 rigid atoms, others: [0, 1, 2, 3, 4, 32, 12, 13, 14, 15, 24, 25, 26, 28, 29, 30, 31] set([33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 27]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061844 none CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)CC#N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 65, 65, 65, 122, 122, 33, 33, 33, 33, 33, 33, 1, 33, 33, 33, 33, 33, 65, 122, 122] 122 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 434 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061844 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061844 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061844/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061844 Building REAL250005061845 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061845' /scratch/stefan/7916143/working/building/REAL250005061845 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061845 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061845/0 /scratch/stefan/7916143/working/building/REAL250005061845 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/982 `/scratch/stefan/7916143/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)CCF) `REAL250005061845.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061845 none CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 5, 15, 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, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 43, 43, 43, 43, 43, 1, 1, 1, 1, 5, 5, 5, 33, 66, 2, 2, 2, 1, 1, 1, 43, 1, 1, 1, 1, 1, 5, 33, 33, 66, 66] 185 rigid atoms, others: [0, 1, 2, 3, 4, 32, 12, 13, 14, 15, 24, 25, 26, 28, 29, 30, 31] set([33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 27, 37]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061845 none CC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1NC(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 5, 15, 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, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 11, 1, 11, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 94, 94, 94, 185, 185, 43, 43, 43, 43, 43, 43, 1, 43, 43, 43, 43, 43, 94, 185, 185, 185, 185] 185 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 643 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061845 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061845 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061845/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061845 Building REAL250005061846 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061846' /scratch/stefan/7916143/working/building/REAL250005061846 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061846 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061846/0 /scratch/stefan/7916143/working/building/REAL250005061846 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/983 `/scratch/stefan/7916143/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C) `REAL250005061846.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061846 none C[C@@H](O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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 213 conformations in input total number of sets (complete confs): 213 using faster count positions algorithm for large data unique positions, atoms: [26, 6, 26, 26, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 32, 1, 1, 1, 26, 26, 26, 78, 6, 1, 1, 1, 1, 1, 32, 1, 1, 1, 2, 2, 2] 213 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 32, 36, 37, 38]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061846 none C[C@@H](O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C 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', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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 213 conformations in input total number of sets (complete confs): 213 using faster count positions algorithm for large data unique positions, atoms: [71, 51, 71, 71, 51, 51, 32, 32, 32, 32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 32, 32, 32, 71, 71, 71, 213, 51, 32, 32, 32, 32, 32, 1, 32, 32, 32, 32, 32, 32] 213 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061846 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061846 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061846/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061846 Building REAL250005061847 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061847' /scratch/stefan/7916143/working/building/REAL250005061847 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061847 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061847/0 /scratch/stefan/7916143/working/building/REAL250005061847 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/984 `/scratch/stefan/7916143/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C) `REAL250005061847.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061847 none C=CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 1, 19, 19, 19, 5, 1, 1, 1, 1, 1, 37, 1, 1, 1, 2, 2, 2] 58 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 33, 10, 11, 12, 13, 14, 15, 16, 34, 35, 20, 21, 22, 23, 29]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061847 none C=CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 37, 37, 37, 37, 11, 1, 11, 1, 1, 1, 1, 1, 1, 37, 37, 37, 58, 58, 58, 58, 37, 37, 37, 37, 37, 1, 37, 37, 37, 37, 37, 37] 58 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 128 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061847 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061847 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061847/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061847 Building REAL250005061848 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061848' /scratch/stefan/7916143/working/building/REAL250005061848 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061848 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061848/0 /scratch/stefan/7916143/working/building/REAL250005061848 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/985 `/scratch/stefan/7916143/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCCCC1CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005061848.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061848 none CCC(=O)N1CCCCC1CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 7, 28, 28, 28, 39, 39, 39, 39, 39, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 28, 39] 47 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 34, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061848 none CCC(=O)N1CCCCC1CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 43, 39, 43, 39, 39, 39, 39, 39, 30, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 39, 39, 39, 39, 39, 39, 39, 39, 39, 31, 31, 21, 21, 8, 1] 47 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: 203 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061848 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061848 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061848/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061848 Building REAL250005061849 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061849' /scratch/stefan/7916143/working/building/REAL250005061849 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061849 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061849/0 /scratch/stefan/7916143/working/building/REAL250005061849 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/986 `/scratch/stefan/7916143/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCCC1CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005061849.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061849 none CC(=O)N1CCCCC1CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 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, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 7, 19, 19, 19, 23, 23, 23, 23, 23, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 19, 23] 23 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 34, 36, 37, 35, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 78 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061849 none CC(=O)N1CCCCC1CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 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, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 20, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 20, 20, 18, 18, 8, 1] 23 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: 83 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061849 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061849 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061849/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061849 Building REAL250005061850 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061850' /scratch/stefan/7916143/working/building/REAL250005061850 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061850 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061850/0 /scratch/stefan/7916143/working/building/REAL250005061850 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/987 `/scratch/stefan/7916143/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CCCCC1CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005061850.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061850 none O=C(CO)N1CCCCC1CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 10, 1, 1, 1, 1, 1, 1, 1, 3, 8, 31, 31, 31, 41, 41, 41, 41, 41, 10, 10, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 31, 41] 153 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38]) total number of confs: 170 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061850 none O=C(CO)N1CCCCC1CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [44, 41, 44, 51, 41, 41, 41, 41, 41, 32, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 51, 51, 153, 41, 41, 41, 41, 41, 41, 41, 41, 41, 33, 33, 26, 26, 7, 1] 153 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: 364 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061850 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061850 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061850/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061850 Building REAL250005061851 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061851' /scratch/stefan/7916143/working/building/REAL250005061851 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061851 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061851/0 /scratch/stefan/7916143/working/building/REAL250005061851 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/988 `/scratch/stefan/7916143/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCCC1CCCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005061851.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061851 none CCC(=O)NCCC1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [73, 28, 28, 28, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 17, 17, 17, 17, 73, 73, 73, 73, 73, 28, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17] 109 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 39, 38, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40]) total number of confs: 311 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061851 none CCC(=O)NCCC1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 83, 83, 83, 41, 26, 17, 17, 17, 17, 17, 17, 11, 1, 11, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 83, 41, 41, 26, 26, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1] 109 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: 453 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061851 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061851 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061851/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061851 Building REAL250005061852 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061852' /scratch/stefan/7916143/working/building/REAL250005061852 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061852 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061852/0 /scratch/stefan/7916143/working/building/REAL250005061852 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/989 `/scratch/stefan/7916143/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCC1CCCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005061852.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061852 none CC(=O)NCCC1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 16, 16, 16, 16, 19, 19, 19, 19, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16] 36 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061852 none CC(=O)NCCC1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 29, 22, 16, 16, 16, 16, 16, 16, 11, 1, 11, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 29, 29, 22, 22, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1] 36 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: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061852 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061852 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061852/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061852 Building REAL250005061853 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061853' /scratch/stefan/7916143/working/building/REAL250005061853 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061853 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061853/0 /scratch/stefan/7916143/working/building/REAL250005061853 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/990 `/scratch/stefan/7916143/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NCCC1CCCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005061853.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061853 none O=C(CO)NCCC1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 51, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 13, 13, 51, 51, 153, 26, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13] 177 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061853 none O=C(CO)NCCC1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 59, 27, 20, 13, 13, 13, 13, 13, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 59, 59, 177, 54, 27, 27, 20, 20, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1] 177 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: 406 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061853 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061853 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061853/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061853 Building REAL250005061854 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061854' /scratch/stefan/7916143/working/building/REAL250005061854 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061854 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061854/0 /scratch/stefan/7916143/working/building/REAL250005061854 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/991 `/scratch/stefan/7916143/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NCCC1CCCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005061854.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061854 none C=CC(=O)NCCC1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [47, 29, 29, 29, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 19, 19, 19, 19, 19, 47, 47, 47, 29, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19] 72 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061854 none C=CC(=O)NCCC1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 43, 28, 19, 19, 19, 19, 19, 19, 12, 1, 12, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 43, 43, 28, 28, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 72 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: 282 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061854 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061854 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061854/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061854 Building REAL250005061855 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061855' /scratch/stefan/7916143/working/building/REAL250005061855 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061855 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061855/0 /scratch/stefan/7916143/working/building/REAL250005061855 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/992 `/scratch/stefan/7916143/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCCC(C(C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061855.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061855 none CCC(=O)N1CCCC(C(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 25, 25, 25, 39, 39, 39, 39, 39, 1, 19, 19, 19, 18, 18, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 25, 39, 1, 1] 64 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 39, 40, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38]) total number of confs: 170 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061855 none CCC(=O)N1CCCC(C(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 39, 64, 39, 39, 39, 39, 16, 6, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 39, 64, 64, 64, 64, 64, 39, 39, 39, 39, 39, 39, 39, 16, 16, 16, 16, 6, 1, 39, 39] 64 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: 193 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061855 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061855 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061855/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061855 Building REAL250005061856 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061856' /scratch/stefan/7916143/working/building/REAL250005061856 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061856 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061856/0 /scratch/stefan/7916143/working/building/REAL250005061856 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/993 `/scratch/stefan/7916143/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC(C(C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061856.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061856 none CC(=O)N1CCCC(C(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 27, 27, 27, 27, 27, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 22, 27, 1, 1] 35 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 37, 19, 23, 24, 25, 26, 27, 28, 29, 36] set([0, 32, 2, 34, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 35, 20, 21, 22, 30, 31]) total number of confs: 88 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061856 none CC(=O)N1CCCC(C(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 27, 35, 27, 27, 27, 27, 15, 8, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 27, 35, 35, 35, 27, 27, 27, 27, 27, 27, 27, 15, 15, 15, 15, 8, 1, 27, 27] 35 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: 113 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061856 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061856 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061856/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061856 Building REAL250005061857 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061857' /scratch/stefan/7916143/working/building/REAL250005061857 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061857 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061857/0 /scratch/stefan/7916143/working/building/REAL250005061857 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/994 `/scratch/stefan/7916143/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(=O)C1=CC(=O)[N-]O1)C1CCCN(C(=O)CO)C1) `REAL250005061857.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061857 none CC(NC(=O)C1=CC(=O)[N-]O1)C1CCCN(C(=O)CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 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 234 conformations in input total number of sets (complete confs): 234 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 44, 44, 44, 44, 44, 77, 77, 78, 43, 15, 15, 15, 15, 6, 1, 44, 44, 44, 44, 44, 44, 44, 78, 78, 234, 44, 44] 234 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 487 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061857 none CC(NC(=O)C1=CC(=O)[N-]O1)C1CCCN(C(=O)CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 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 234 conformations in input total number of sets (complete confs): 234 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 32, 32, 32, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 7, 7, 19, 1, 10, 10, 10, 9, 32, 44, 1, 1, 1, 1, 1, 1, 1, 19, 19, 57, 1, 1] 234 rigid atoms, others: [32, 1, 37, 38, 33, 11, 12, 13, 14, 15, 16, 20, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 21, 22, 23, 24, 25, 26, 34, 35, 36]) total number of confs: 242 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061857 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061857 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061857/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061857 Building REAL250005061858 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061858' /scratch/stefan/7916143/working/building/REAL250005061858 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061858 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061858/0 /scratch/stefan/7916143/working/building/REAL250005061858 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/995 `/scratch/stefan/7916143/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC(C)C1CCCN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061858.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061858 none CCC(=O)NC(C)C1CCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [74, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 42, 42, 42, 42, 42, 1, 74, 74, 74, 74, 74, 19, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 42, 1, 1] 147 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 40, 20, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38]) total number of confs: 332 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061858 none CCC(=O)NC(C)C1CCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 121, 121, 121, 96, 42, 96, 42, 42, 42, 42, 11, 1, 11, 1, 1, 1, 1, 1, 1, 42, 147, 147, 147, 147, 147, 121, 96, 96, 96, 96, 42, 42, 42, 42, 42, 42, 42, 1, 42, 42] 147 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: 539 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061858 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061858 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061858/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061858 Building REAL250005061859 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061859' /scratch/stefan/7916143/working/building/REAL250005061859 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061859 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061859/0 /scratch/stefan/7916143/working/building/REAL250005061859 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/996 `/scratch/stefan/7916143/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)C1CCCN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061859.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061859 none CC(=O)NC(C)C1CCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 13, 13, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 21, 1, 1] 39 rigid atoms, others: [32, 33, 34, 4, 37, 6, 7, 8, 9, 10, 11, 19, 36, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 35, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061859 none CC(=O)NC(C)C1CCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 35, 21, 35, 21, 21, 21, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 39, 39, 39, 39, 35, 35, 35, 35, 21, 21, 21, 21, 21, 21, 21, 1, 21, 21] 39 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: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061859 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061859 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061859/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061859 Building REAL250005061860 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061860' /scratch/stefan/7916143/working/building/REAL250005061860 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061860 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061860/0 /scratch/stefan/7916143/working/building/REAL250005061860 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/997 `/scratch/stefan/7916143/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(=O)CO)C1CCCN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061860.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061860 none CC(NC(=O)CO)C1CCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 231 conformations in input total number of sets (complete confs): 231 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 17, 17, 17, 36, 1, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 8, 8, 8, 8, 17, 36, 36, 108, 1, 1, 1, 1, 1, 1, 1, 35, 1, 1] 231 rigid atoms, others: [32, 1, 34, 35, 33, 38, 7, 8, 9, 10, 11, 12, 37, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 296 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061860 none CC(NC(=O)CO)C1CCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 231 conformations in input total number of sets (complete confs): 231 using faster count positions algorithm for large data unique positions, atoms: [71, 35, 71, 77, 77, 77, 77, 35, 35, 35, 35, 11, 1, 11, 1, 1, 1, 1, 1, 1, 35, 71, 71, 71, 71, 77, 77, 77, 231, 35, 35, 35, 35, 35, 35, 35, 1, 35, 35] 231 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 470 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061860 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061860 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061860/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061860 Building REAL250005061861 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061861' /scratch/stefan/7916143/working/building/REAL250005061861 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061861 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061861/0 /scratch/stefan/7916143/working/building/REAL250005061861 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/998 `/scratch/stefan/7916143/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NC(C)C1CCCN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005061861.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061861 none C=CC(=O)NC(C)C1CCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [45, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 39, 39, 39, 39, 39, 1, 45, 45, 45, 21, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 39, 1, 1] 98 rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 12, 37, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 189 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061861 none C=CC(=O)NC(C)C1CCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 80, 39, 80, 39, 39, 39, 39, 12, 1, 12, 1, 1, 1, 1, 1, 1, 39, 98, 98, 98, 98, 80, 80, 80, 80, 39, 39, 39, 39, 39, 39, 39, 1, 39, 39] 98 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: 307 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061861 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061861 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061861/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061861 Building REAL250005061862 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061862' /scratch/stefan/7916143/working/building/REAL250005061862 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061862 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061862/0 /scratch/stefan/7916143/working/building/REAL250005061862 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/999 `/scratch/stefan/7916143/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCCC(C)C1CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061862.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061862 none CCC(=O)N1CCCC(C)C1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 20, 20, 20, 20, 20, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 13, 20] 20 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 11, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061862 none CCC(=O)N1CCCC(C)C1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 13, 4, 1] 20 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: 70 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061862 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061862 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061862/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061862 Building REAL250005061863 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061863' /scratch/stefan/7916143/working/building/REAL250005061863 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061863 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061863/0 /scratch/stefan/7916143/working/building/REAL250005061863 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1000 `/scratch/stefan/7916143/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC(C)C1CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061863.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061863 none CC(=O)N1CCCC(C)C1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 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, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 15, 15, 15, 15, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 12, 15] 15 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 33, 23, 24, 25, 26, 27, 28, 29] set([0, 32, 2, 34, 36, 37, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31]) total number of confs: 51 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061863 none CC(=O)N1CCCC(C)C1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 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, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 5, 1] 15 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: 52 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061863 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061863 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061863/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061863 Building REAL250005061864 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061864' /scratch/stefan/7916143/working/building/REAL250005061864 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061864 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061864/0 /scratch/stefan/7916143/working/building/REAL250005061864 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1001 `/scratch/stefan/7916143/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCN(C(=O)CO)C1CNC(=O)C1=CC(=O)[N-]O1) `REAL250005061864.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061864 none CC1CCCN(C(=O)CO)C1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 1, 1, 5, 12, 12, 12, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 1, 5, 5, 12, 19] 75 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 10, 11, 34, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 111 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061864 none CC1CCCN(C(=O)CO)C1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 20, 20, 25, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 25, 25, 75, 19, 13, 13, 6, 1] 75 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: 171 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061864 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061864 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061864/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061864 Building REAL250005061865 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061865' /scratch/stefan/7916143/working/building/REAL250005061865 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061865 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061865/0 /scratch/stefan/7916143/working/building/REAL250005061865 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1002 `/scratch/stefan/7916143/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC1C(C)CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005061865.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061865 none CCC(=O)NCC1C(C)CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 10, 10, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 11, 23, 23, 23, 23, 23, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11] 27 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 37, 39, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 105 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061865 none CCC(=O)NCC1C(C)CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 18, 18, 14, 11, 11, 11, 11, 11, 11, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 18, 14, 14, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1] 27 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: 111 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061865 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061865 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061865/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061865 Building REAL250005061866 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061866' /scratch/stefan/7916143/working/building/REAL250005061866 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061866 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061866/0 /scratch/stefan/7916143/working/building/REAL250005061866 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1003 `/scratch/stefan/7916143/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1C(C)CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005061866.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061866 none CC(=O)NCC1C(C)CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 7, 7, 7, 7, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6] 11 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 36, 26, 27, 31] set([0, 1, 2, 3, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061866 none CC(=O)NCC1C(C)CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1] 11 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: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061866 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061866 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061866/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061866 Building REAL250005061867 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061867' /scratch/stefan/7916143/working/building/REAL250005061867 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061867 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061867/0 /scratch/stefan/7916143/working/building/REAL250005061867 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1004 `/scratch/stefan/7916143/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCN(C(=O)C2=CC(=O)[N-]O2)C1CNC(=O)CO) `REAL250005061867.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061867 none CC1CCCN(C(=O)C2=CC(=O)[N-]O2)C1CNC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 11, 1, 1, 5, 10, 10, 10, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 5, 5, 10, 25, 25, 75] 87 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 31]) total number of confs: 183 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061867 none CC1CCCN(C(=O)C2=CC(=O)[N-]O2)C1CNC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 1, 1, 1, 11, 11, 17, 22, 22, 22, 29, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 11, 17, 17, 22, 29, 29, 87] 87 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 206 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061867 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061867 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061867/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061867 Building REAL250005061868 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061868' /scratch/stefan/7916143/working/building/REAL250005061868 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061868 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061868/0 /scratch/stefan/7916143/working/building/REAL250005061868 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1005 `/scratch/stefan/7916143/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)NCC1C(C)CCCN1C(=O)C1=CC(=O)[N-]O1) `REAL250005061868.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061868 none C=CC(=O)NCC1C(C)CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 12, 13, 13, 13, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12] 20 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 37, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 59 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061868 none C=CC(=O)NCC1C(C)CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 16, 12, 12, 12, 12, 12, 12, 12, 11, 1, 11, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 16, 16, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1] 20 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: 65 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061868 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061868 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061868/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061868 Building REAL250005061869 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061869' /scratch/stefan/7916143/working/building/REAL250005061869 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061869 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061869/0 /scratch/stefan/7916143/working/building/REAL250005061869 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1006 `/scratch/stefan/7916143/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(CCN(C)C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005061869.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061869 none CC(=O)N1CCC(CCN(C)C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 8, 12, 35, 35, 105, 105, 146, 146, 146, 146, 146, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 12, 12, 35, 35, 35, 146, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 40, 19, 20, 24, 25, 26, 27, 28, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 397 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061869 none CC(=O)N1CCC(CCN(C)C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 11, 8, 5, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 146, 201, 146, 146, 146, 76, 66, 27, 10, 27, 1, 10, 1, 1, 1, 1, 1, 1, 146, 146, 201, 201, 201, 146, 146, 146, 146, 146, 82, 82, 66, 66, 27, 27, 27, 1, 146, 146, 146, 146] 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: 770 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061869 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061869 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061869/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061869 Building REAL250005061870 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061870' /scratch/stefan/7916143/working/building/REAL250005061870 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061870 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061870/0 /scratch/stefan/7916143/working/building/REAL250005061870 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1007 `/scratch/stefan/7916143/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005061870.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061870 none CC(=O)N(C)CCC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [45, 29, 45, 12, 29, 8, 1, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 45, 45, 45, 29, 29, 29, 12, 12, 8, 8, 1, 1, 1, 1, 1, 33, 1, 1, 1, 1] 165 rigid atoms, others: [32, 33, 34, 35, 37, 6, 7, 8, 9, 10, 11, 40, 19, 20, 39, 38, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 203 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061870 none CC(=O)N(C)CCC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 115, 165, 89, 33, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 165, 165, 165, 165, 165, 165, 115, 115, 89, 89, 33, 33, 33, 33, 33, 1, 33, 33, 33, 33] 165 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: 651 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061870 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061870 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061870/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061870 Building REAL250005061871 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061871' /scratch/stefan/7916143/working/building/REAL250005061871 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061871 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061871/0 /scratch/stefan/7916143/working/building/REAL250005061871 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1008 `/scratch/stefan/7916143/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005061871.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061871 none CCC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [179, 128, 128, 128, 61, 22, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 22, 62, 62, 179, 179, 179, 179, 179, 128, 61, 61, 22, 12, 1, 64, 64, 64, 64, 64, 64, 64] 185 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 899 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061871 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061871 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061871/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061871 Building REAL250005061872 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061872' /scratch/stefan/7916143/working/building/REAL250005061872 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061872 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061872/0 /scratch/stefan/7916143/working/building/REAL250005061872 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1009 `/scratch/stefan/7916143/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005061872.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061872 none COCCC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 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 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [142, 136, 115, 67, 67, 67, 27, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 28, 29, 142, 142, 142, 136, 136, 115, 115, 67, 27, 27, 11, 5, 1, 29, 29, 29, 29, 29, 29, 29] 147 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: 666 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061872 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061872 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061872/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061872 Building REAL250005061873 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061873' /scratch/stefan/7916143/working/building/REAL250005061873 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061873 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061873/0 /scratch/stefan/7916143/working/building/REAL250005061873 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1010 `/scratch/stefan/7916143/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005061873.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061873 none CC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 34, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 15, 30, 31, 47, 47, 47, 47, 34, 34, 15, 9, 1, 31, 31, 31, 31, 31, 31, 31] 48 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 248 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061873 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061873 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061873/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061873 Building REAL250005061874 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061874' /scratch/stefan/7916143/working/building/REAL250005061874 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061874 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061874/0 /scratch/stefan/7916143/working/building/REAL250005061874 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1011 `/scratch/stefan/7916143/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CNC(=O)C1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061874.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061874 none CC(C)C(CNC(=O)C1CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 137, 177, 57, 13, 13, 1, 13, 1, 1, 1, 137, 179, 179, 179, 197, 197, 197, 197, 197, 177, 177, 177, 177, 177, 177, 177, 137, 57, 57, 13, 1, 1, 1, 1, 1, 179, 197] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 31] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37]) total number of confs: 963 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061874 none CC(C)C(CNC(=O)C1CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 17, 47, 7, 17, 46, 100, 100, 100, 194, 194, 7, 1, 7, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 17, 46, 46, 100, 194, 194, 194, 194, 194, 7, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 760 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061874 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061874 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061874/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061874 Building REAL250005061875 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061875' /scratch/stefan/7916143/working/building/REAL250005061875 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061875 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061875/0 /scratch/stefan/7916143/working/building/REAL250005061875 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1012 `/scratch/stefan/7916143/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CNC(=O)C1CCC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061875.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061875 none CC(C)C(CNC(=O)C1CCC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [178, 129, 178, 56, 11, 11, 1, 11, 1, 1, 1, 1, 129, 171, 171, 171, 193, 193, 193, 193, 193, 178, 178, 178, 178, 178, 178, 178, 129, 56, 56, 11, 1, 1, 1, 1, 1, 1, 1, 171, 193] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40]) total number of confs: 940 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061875 none CC(C)C(CNC(=O)C1CCC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 20, 53, 8, 20, 54, 115, 115, 115, 193, 193, 193, 8, 1, 8, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 20, 54, 54, 115, 193, 193, 193, 193, 193, 193, 193, 8, 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: 797 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061875 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061875 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061875/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061875 Building REAL250005061876 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061876' /scratch/stefan/7916143/working/building/REAL250005061876 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061876 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061876/0 /scratch/stefan/7916143/working/building/REAL250005061876 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1013 `/scratch/stefan/7916143/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CNC(=O)CC1CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061876.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061876 none CC(C)C(CNC(=O)CC1CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 168, 191, 99, 23, 23, 3, 23, 1, 1, 1, 1, 168, 198, 198, 198, 199, 199, 199, 199, 199, 191, 191, 191, 191, 191, 191, 191, 168, 99, 99, 23, 3, 3, 1, 1, 1, 1, 1, 198, 199] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 32, 33, 39, 40]) total number of confs: 965 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061876 none CC(C)C(CNC(=O)CC1CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 10, 27, 4, 10, 29, 71, 71, 71, 168, 199, 199, 4, 1, 4, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 10, 29, 29, 71, 168, 168, 199, 199, 199, 199, 199, 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: 870 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061876 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061876 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061876/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061876 Building REAL250005061877 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061877' /scratch/stefan/7916143/working/building/REAL250005061877 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061877 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061877/0 /scratch/stefan/7916143/working/building/REAL250005061877 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1014 `/scratch/stefan/7916143/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005061877.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061877 none COCC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 182, 75, 75, 75, 28, 11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 30, 30, 193, 193, 193, 182, 182, 75, 28, 28, 11, 6, 1, 31, 31, 31, 31, 31, 31, 31] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 808 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061877 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061877 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061877/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061877 Building REAL250005061878 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061878' /scratch/stefan/7916143/working/building/REAL250005061878 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061878 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061878/0 /scratch/stefan/7916143/working/building/REAL250005061878 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1015 `/scratch/stefan/7916143/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005061878.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061878 none CCCC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 175, 87, 87, 87, 32, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 27, 26, 194, 194, 194, 194, 194, 175, 175, 87, 32, 32, 10, 4, 1, 28, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 936 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061878 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061878 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061878/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061878 Building REAL250005061879 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061879' /scratch/stefan/7916143/working/building/REAL250005061879 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061879 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061879/0 /scratch/stefan/7916143/working/building/REAL250005061879 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1016 `/scratch/stefan/7916143/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005061879.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061879 none CC(C)CC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [183, 182, 190, 98, 98, 98, 45, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 40, 40, 190, 190, 190, 190, 190, 190, 190, 182, 182, 98, 45, 45, 15, 7, 1, 41, 41, 41, 41, 41, 41, 41] 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: 938 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061879 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061879 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061879/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061879 Building REAL250005061880 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061880' /scratch/stefan/7916143/working/building/REAL250005061880 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061880 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061880/0 /scratch/stefan/7916143/working/building/REAL250005061880 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1017 `/scratch/stefan/7916143/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CNC(=O)C1CC1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061880.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061880 none CC(C)C(CNC(=O)C1CC1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 131, 179, 58, 13, 13, 1, 13, 1, 1, 1, 1, 131, 172, 172, 172, 193, 193, 193, 193, 193, 179, 179, 179, 179, 179, 179, 179, 131, 58, 58, 13, 1, 1, 1, 1, 2, 2, 2, 172, 193] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 1004 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061880 none CC(C)C(CNC(=O)C1CC1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 18, 40, 8, 18, 45, 97, 97, 97, 193, 193, 193, 8, 1, 8, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 18, 45, 45, 97, 193, 193, 193, 193, 193, 193, 193, 8, 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: 731 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061880 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061880 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061880/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061880 Building REAL250005061881 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061881' /scratch/stefan/7916143/working/building/REAL250005061881 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061881 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061881/0 /scratch/stefan/7916143/working/building/REAL250005061881 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1018 `/scratch/stefan/7916143/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005061881.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061881 none CCOCC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [196, 188, 139, 107, 107, 107, 40, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 38, 39, 196, 196, 196, 196, 196, 143, 143, 107, 40, 40, 14, 6, 1, 39, 39, 39, 39, 39, 39, 39] 198 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: 773 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061881 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061881 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061881/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061881 Building REAL250005061882 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061882' /scratch/stefan/7916143/working/building/REAL250005061882 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061882 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061882/0 /scratch/stefan/7916143/working/building/REAL250005061882 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1019 `/scratch/stefan/7916143/working/3D/1019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005061882.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061882 none CC(C)=CC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [156, 156, 156, 103, 103, 103, 50, 20, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 48, 48, 156, 156, 156, 156, 156, 156, 156, 103, 50, 50, 20, 9, 1, 49, 49, 49, 49, 49, 49, 49] 166 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: 669 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061882 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061882 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061882/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061882 Building REAL250005061883 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061883' /scratch/stefan/7916143/working/building/REAL250005061883 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061883 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061883/0 /scratch/stefan/7916143/working/building/REAL250005061883 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1020 `/scratch/stefan/7916143/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005061883.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061883 none CCCCC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [159, 154, 149, 54, 54, 54, 37, 14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 37, 40, 159, 159, 159, 159, 159, 159, 159, 149, 149, 54, 37, 37, 14, 7, 1, 40, 40, 40, 40, 40, 40, 40] 186 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: 802 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061883 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061883 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061883/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061883 Building REAL250005061884 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061884' /scratch/stefan/7916143/working/building/REAL250005061884 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061884 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061884/0 /scratch/stefan/7916143/working/building/REAL250005061884 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1021 `/scratch/stefan/7916143/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005061884.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061884 none CC(C)C(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 127, 195, 127, 127, 59, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 62, 62, 195, 195, 195, 195, 195, 195, 195, 127, 59, 59, 22, 9, 1, 65, 65, 65, 65, 65, 65, 65] 201 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 970 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061884 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061884 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061884/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061884 Building REAL250005061885 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061885' /scratch/stefan/7916143/working/building/REAL250005061885 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061885 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061885/0 /scratch/stefan/7916143/working/building/REAL250005061885 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1022 `/scratch/stefan/7916143/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005061885.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061885 none CCC(C)C(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 181, 88, 181, 88, 88, 36, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 37, 37, 193, 193, 193, 193, 193, 181, 181, 181, 181, 88, 36, 36, 15, 7, 1, 38, 38, 38, 38, 38, 38, 38] 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: 892 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061885 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061885 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061885/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061885 Building REAL250005061886 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061886' /scratch/stefan/7916143/working/building/REAL250005061886 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061886 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061886/0 /scratch/stefan/7916143/working/building/REAL250005061886 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1023 `/scratch/stefan/7916143/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005061886.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061886 none COC(C)C(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 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, 183, 82, 183, 82, 82, 31, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 31, 31, 192, 192, 192, 183, 183, 183, 183, 82, 31, 31, 15, 8, 1, 32, 32, 32, 32, 32, 32, 32] 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: 786 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061886 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061886 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061886/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061886 Building REAL250005061887 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061887' /scratch/stefan/7916143/working/building/REAL250005061887 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061887 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061887/0 /scratch/stefan/7916143/working/building/REAL250005061887 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1024 `/scratch/stefan/7916143/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005061887.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061887 none C=CCCC(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 189, 150, 66, 66, 66, 38, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 37, 38, 195, 195, 195, 189, 189, 150, 150, 66, 38, 38, 17, 7, 1, 38, 38, 38, 38, 38, 38, 38] 201 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 924 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061887 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061887 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061887/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061887 Building REAL250005061888 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061888' /scratch/stefan/7916143/working/building/REAL250005061888 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061888 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061888/0 /scratch/stefan/7916143/working/building/REAL250005061888 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1025 `/scratch/stefan/7916143/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005061888.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061888 none CC=C(C)C(=O)NCC(NC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 107, 193, 107, 107, 48, 18, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 49, 49, 193, 193, 193, 193, 193, 193, 193, 107, 48, 48, 18, 9, 1, 51, 51, 51, 51, 51, 51, 51] 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: 775 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061888 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061888 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061888/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061888 Building REAL250005061889 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061889' /scratch/stefan/7916143/working/building/REAL250005061889 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061889 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061889/0 /scratch/stefan/7916143/working/building/REAL250005061889 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1026 `/scratch/stefan/7916143/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CNC(=O)C1(C)CC1)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061889.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061889 none CC(C)C(CNC(=O)C1(C)CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 111, 163, 39, 7, 7, 1, 7, 1, 1, 1, 1, 111, 162, 162, 162, 190, 190, 190, 190, 190, 163, 163, 163, 163, 163, 163, 163, 111, 39, 39, 7, 2, 2, 2, 1, 1, 1, 1, 162, 190] 201 rigid atoms, others: [35, 36, 37, 6, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40]) total number of confs: 936 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061889 none CC(C)C(CNC(=O)C1(C)CC1)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 20, 48, 9, 20, 48, 96, 96, 96, 190, 190, 190, 9, 1, 9, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 20, 48, 48, 96, 190, 190, 190, 190, 190, 190, 190, 9, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 765 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061889 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061889 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061889/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061889 Building REAL250005061890 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061890' /scratch/stefan/7916143/working/building/REAL250005061890 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061890 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061890/0 /scratch/stefan/7916143/working/building/REAL250005061890 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1027 `/scratch/stefan/7916143/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CNC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061890.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061890 none CC(C)C(CNC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 129, 174, 57, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 129, 174, 174, 174, 193, 193, 193, 193, 193, 175, 175, 175, 175, 175, 174, 175, 129, 57, 57, 12, 1, 1, 2, 2, 2, 174, 193] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 960 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061890 none CC(C)C(CNC(=O)[C@@H]1C[C@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 18, 42, 6, 18, 47, 93, 93, 93, 193, 193, 193, 193, 193, 7, 1, 6, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 18, 47, 47, 93, 193, 193, 193, 193, 193, 7, 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: 740 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061890 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061890 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061890/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061890 Building REAL250005061891 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061891' /scratch/stefan/7916143/working/building/REAL250005061891 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061891 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061891/0 /scratch/stefan/7916143/working/building/REAL250005061891 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1028 `/scratch/stefan/7916143/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CNC(=O)[C@H]1C[C@@H]1C)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061891.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061891 none CC(C)C(CNC(=O)[C@H]1C[C@@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 132, 179, 58, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 132, 173, 173, 173, 193, 193, 193, 193, 193, 179, 179, 179, 179, 179, 179, 179, 132, 58, 58, 13, 1, 1, 2, 2, 2, 173, 193] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 1000 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061891 none CC(C)C(CNC(=O)[C@H]1C[C@@H]1C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 18, 39, 8, 18, 44, 97, 97, 97, 193, 193, 193, 193, 193, 8, 1, 8, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 18, 44, 44, 97, 193, 193, 193, 193, 193, 8, 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: 729 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061891 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061891 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061891/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061891 Building REAL250005061892 mkdir: created directory `/scratch/stefan/7916143/working/building/REAL250005061892' /scratch/stefan/7916143/working/building/REAL250005061892 /scratch/stefan/7916143/working /scratch/stefan/7916143 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005061892 mkdir: created directory `0' /scratch/stefan/7916143/working/building/REAL250005061892/0 /scratch/stefan/7916143/working/building/REAL250005061892 /scratch/stefan/7916143/working /scratch/stefan/7916143 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7916143/working/3D/1029 `/scratch/stefan/7916143/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CNC(=O)C(N)=O)NC(=O)C1=CC(=O)[N-]O1) `REAL250005061892.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005061892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916143/working/building/REAL250005061892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005061892 none CC(C)C(CNC(=O)C(N)=O)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 6, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [49, 22, 48, 10, 22, 53, 107, 107, 107, 129, 130, 10, 1, 10, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 22, 53, 53, 107, 130, 129, 10, 1] 137 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: 582 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916143/working/building/REAL250005061892 /scratch/stefan/7916143/working /scratch/stefan/7916143 Finished preparing REAL250005061892 Recording results /scratch/stefan/7916143/working /scratch/stefan/7916143 Appending to /scratch/stefan/7916143/finished/xaaaaax.* 0: /scratch/stefan/7916143/working/building/REAL250005061892/0.* Removing working files in /scratch/stefan/7916143/working/building/REAL250005061892 /scratch/stefan/7916143 Compressing combined databse files /scratch/stefan/7916143/finished/xaaaaax.db2.gz /scratch/stefan/7916143/finished/xaaaaax.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7916143/finished) ======================================================= Finalizing... removed `/scratch/stefan/7916143/working/3D/1030' removed directory: `/scratch/stefan/7916143/working/3D' `/scratch/stefan/7916143/working/protonate' -> `/scratch/stefan/7916143/archive' `/scratch/stefan/7916143/working/input-smiles.ism' -> `/scratch/stefan/7916143/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7916143/working/building' rmdir: removing directory, `/scratch/stefan/7916143/working' ls: No match. ls: No match.